Contacts of the helix formed by residues 289 - 312 (chain B) in PDB entry 1H4R
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with LYS 289 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71B THR* 5.1 0.7 - - - +
287B SER* 3.6 2.8 + - - -
288B SER* 1.3 86.8 + - - +
290B LEU* 1.3 60.3 + - - +
291B ARG* 3.6 39.5 - - - +
292B VAL* 3.1 30.3 + - + +
293B ASN* 2.9 33.6 + - - +
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Residues in contact with LEU 290 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
266B TYR* 4.2 21.8 - - + +
288B SER 3.6 4.6 + - - -
289B LYS* 1.3 71.6 - - - +
291B ARG* 1.3 59.4 + - - +
293B ASN* 3.1 8.1 + - - +
294B LYS* 2.9 57.5 + - + +
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Residues in contact with ARG 291 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68B ILE* 4.0 23.6 - - + -
69B LYS* 3.6 50.1 - - - +
70B ASP* 5.0 5.3 - - - +
71B THR* 3.3 36.1 + - + +
72B VAL 5.0 1.0 - - - +
289B LYS* 3.6 39.0 - - + +
290B LEU* 1.3 80.5 - - - +
292B VAL* 1.3 65.9 + - + +
294B LYS* 3.6 10.3 + - - +
295B LEU* 3.3 19.6 + - - +
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Residues in contact with VAL 292 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71B THR* 3.8 29.2 - - + +
222B PHE* 3.5 33.4 - - + -
223B ALA 6.0 0.9 - - - +
287B SER* 4.3 8.3 - - - +
289B LYS* 3.1 34.5 + - + +
291B ARG* 1.3 76.4 - - + +
293B ASN* 1.3 59.4 + - - +
295B LEU* 3.0 5.7 + - - +
296B ILE* 2.8 34.8 + - + +
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Residues in contact with ASN 293 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
266B TYR* 2.6 53.0 + - + +
268B ASP 4.1 0.2 + - - -
269B LYS* 4.4 0.2 - - - +
271B PHE* 3.5 13.9 - - + -
287B SER* 2.5 50.0 + - - -
288B SER 4.7 0.4 - - - -
289B LYS 2.9 18.0 + - - +
290B LEU 3.1 6.0 + - - +
292B VAL* 1.3 77.4 - - - +
294B LYS* 1.3 61.6 + - - +
296B ILE* 3.3 4.2 + - - +
297B LEU* 3.1 29.7 + - - +
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Residues in contact with LYS 294 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
266B TYR* 6.5 1.1 - - + -
290B LEU* 2.9 49.4 + - + +
291B ARG* 3.8 9.8 - - - +
292B VAL 3.2 0.2 - - - -
293B ASN* 1.3 76.1 - - - +
295B LEU* 1.3 62.4 + - - +
297B LEU* 3.4 12.3 + - + +
298B GLN* 3.1 27.8 + - + +
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Residues in contact with LEU 295 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71B THR* 4.6 8.3 - - + -
72B VAL* 3.5 35.9 - - + +
73B ALA* 5.0 0.2 - - - -
74B TRP* 3.8 28.0 - - + +
222B PHE* 3.9 26.2 - - + -
291B ARG 3.3 11.3 + - - +
292B VAL* 3.0 9.8 + - - +
294B LYS* 1.3 77.3 - - - +
296B ILE* 1.3 66.4 + - - +
298B GLN* 3.1 11.2 + - + +
299B LEU* 2.9 41.0 + - + +
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Residues in contact with ILE 296 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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222B PHE* 3.8 45.8 - - + -
224B ILE* 5.4 0.9 - - + -
234B LEU* 4.1 20.6 - - + -
236B VAL* 4.7 2.0 - - + +
271B PHE* 3.7 28.0 - - + -
285B PHE* 5.3 1.3 - - + -
287B SER* 4.3 6.3 - - - +
292B VAL* 2.8 27.0 + - + +
293B ASN* 3.6 18.8 - - - +
295B LEU* 1.3 75.8 - - - +
297B LEU* 1.3 58.3 + - - +
299B LEU* 3.3 5.5 + - - +
300B CYS* 2.9 43.1 + - - -
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Residues in contact with LEU 297 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
264B ILE* 4.4 24.9 - - + +
265B SER* 5.4 0.2 - - - -
266B TYR* 4.1 32.1 - - + +
271B PHE* 4.1 15.9 - - + -
293B ASN 3.1 19.5 + - - +
294B LYS* 3.6 12.3 - - + +
295B LEU 3.2 0.2 - - - -
296B ILE* 1.3 73.6 - - - +
298B GLN* 1.3 66.6 + - - +
300B CYS* 3.3 3.8 + - + +
301B ILE* 3.0 41.7 + - + +
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Residues in contact with GLN 298 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73B ALA* 4.6 2.1 - - - +
74B TRP* 3.4 56.0 + - - +
75B LEU 4.9 2.0 + - - -
76B LYS* 3.5 24.1 + - - +
99B LYS* 4.3 21.1 + - - +
100B PHE* 4.2 3.6 - - - -
294B LYS* 3.1 18.7 + - + +
295B LEU* 3.1 16.6 + - + +
297B LEU* 1.3 76.7 - - - +
299B LEU* 1.3 63.2 + - - +
301B ILE* 4.0 4.9 - - - +
302B GLY* 3.1 21.1 + - - -
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Residues in contact with LEU 299 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74B TRP* 4.6 2.9 - - + +
99B LYS* 3.9 40.4 - - + +
100B PHE* 4.1 7.0 - - + -
220B ASN* 3.7 32.5 - - + +
222B PHE* 3.8 20.0 - - + -
236B VAL* 4.0 13.7 - - + -
295B LEU* 2.9 42.2 + - + +
296B ILE* 3.7 4.3 - - - +
298B GLN* 1.3 77.3 - - - +
300B CYS* 1.3 60.6 + - - +
303B ASN* 2.9 33.1 + - - +
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Residues in contact with CYS 300 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
234B LEU* 5.6 0.2 - - - -
236B VAL* 4.3 3.6 - - - -
241B LEU* 3.7 35.2 - - - -
258B TRP* 3.7 16.7 - - + -
264B ILE* 4.4 25.8 - - + -
296B ILE* 2.9 39.9 + - - +
297B LEU* 3.9 6.7 - - + +
299B LEU* 1.3 69.6 - - - +
301B ILE* 1.3 68.4 + - + +
304B HIS* 2.9 28.1 + - - +
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Residues in contact with ILE 301 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
264B ILE* 5.6 7.0 - - + -
297B LEU* 3.0 32.3 + - + +
298B GLN* 4.0 4.3 - - - +
300B CYS* 1.3 77.6 - - + +
302B GLY* 1.3 64.3 + - - +
304B HIS* 3.8 5.2 + - - +
305B ASP* 3.1 24.5 + - + +
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Residues in contact with GLY 302 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100B PHE* 3.5 28.3 - - - -
298B GLN 3.1 11.8 + - - -
301B ILE* 1.3 74.9 - - - +
303B ASN* 1.3 65.2 + - - +
305B ASP* 3.3 8.8 + - - +
306B LEU* 3.1 27.7 + - - +
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Residues in contact with ASN 303 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100B PHE* 3.6 31.1 - - - +
101B TYR 5.0 1.0 + - - +
220B ASN* 4.4 9.3 - - - +
236B VAL* 3.9 12.1 - - - +
237B ASP 3.4 11.4 + - - +
238B ALA* 3.4 24.4 + - - +
258B TRP* 3.6 23.5 - - + +
299B LEU* 2.9 33.0 + - - +
302B GLY* 1.3 72.1 - - - +
304B HIS* 1.3 67.6 + - - +
306B LEU* 3.4 4.8 + - - +
307B PHE* 3.0 24.4 + - - +
310B ARG* 5.2 0.3 + - - -
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Residues in contact with HIS 304 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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258B TRP* 3.3 55.6 + + + -
259B ASN* 5.2 0.6 - - - -
261B ILE* 4.4 12.1 + - + -
264B ILE* 6.6 0.2 - - + -
300B CYS 2.9 19.7 + - - +
301B ILE* 3.8 5.1 + - - +
303B ASN* 1.3 78.1 - - - +
305B ASP* 1.3 66.9 + - - +
307B PHE* 3.3 2.8 + - - +
308B MET* 3.2 48.3 + - + +
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Residues in contact with ASP 305 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
301B ILE* 3.1 15.8 + - + +
302B GLY* 3.4 12.3 - - - +
304B HIS* 1.3 81.8 + - - +
306B LEU* 1.3 64.9 + - - +
308B MET* 3.2 8.3 + - - +
309B ARG* 2.8 71.1 + - - +
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Residues in contact with LEU 306 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60B TRP* 3.9 37.2 - - + +
61B PHE* 4.2 15.3 - - + -
100B PHE* 3.6 36.3 - - + -
101B TYR 5.6 0.2 - - - +
302B GLY 3.1 14.0 + - - +
303B ASN* 4.1 4.9 - - - +
305B ASP* 1.3 81.8 - - - +
307B PHE* 1.3 65.7 + - - +
309B ARG* 3.7 24.6 - - + +
310B ARG* 2.8 48.8 + - - +
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Residues in contact with PHE 307 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103B GLU* 3.7 0.9 - - - -
238B ALA 3.4 18.8 - - - +
239B LEU* 3.6 23.8 - - + -
257B PRO* 5.0 3.4 - - + -
258B TRP* 3.6 24.5 - + + -
259B ASN* 3.5 43.5 - - + -
303B ASN 3.0 18.6 + - - +
304B HIS 3.4 4.9 - - - +
306B LEU* 1.3 77.7 - - - +
308B MET* 1.3 73.9 + - + +
310B ARG* 3.7 10.1 + - - +
311B ARG* 3.0 74.3 + - - +
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Residues in contact with MET 308 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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259B ASN* 4.1 20.2 - - + +
304B HIS* 3.2 40.2 - - + +
305B ASP* 3.2 6.7 + - - +
306B LEU 3.2 0.2 - - - -
307B PHE* 1.3 93.0 - - + +
309B ARG* 1.3 64.0 + - + +
311B ARG* 2.9 17.3 + - + +
312B LYS 2.8 25.0 + - - +
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Residues in contact with ARG 309 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60B TRP* 3.9 33.7 - - - +
305B ASP* 2.8 54.0 + - - +
306B LEU* 3.1 22.6 + - + +
308B MET* 1.3 77.6 - - + +
310B ARG* 1.3 62.7 + - - +
311B ARG 3.2 1.0 + - - -
312B LYS* 3.9 13.8 + - - +
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Residues in contact with ARG 310 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61B PHE* 4.0 10.1 - - - -
101B TYR 3.8 15.4 + - - -
102B PRO* 3.9 1.8 - - - +
103B GLU* 2.8 56.3 + - - +
108B GLU* 2.8 40.5 + - + +
238B ALA* 3.9 12.3 + - - +
303B ASN 5.2 0.2 + - - -
306B LEU* 2.8 44.6 + - - +
307B PHE* 3.7 8.5 - - - +
309B ARG* 1.3 77.7 - - - +
311B ARG* 1.3 64.6 + - - +
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Residues in contact with ARG 311 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103B GLU* 2.6 42.0 + - - -
239B LEU* 5.4 1.2 - - - +
259B ASN* 4.8 8.3 - - - +
307B PHE* 3.0 65.2 + - - +
308B MET* 2.9 15.2 + - + +
310B ARG* 1.3 84.0 - - - +
312B LYS* 1.3 65.0 + - - +
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Residues in contact with LYS 312 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
308B MET* 2.8 20.5 + - - +
309B ARG* 4.1 11.4 - - - +
310B ARG 4.8 0.2 - - - -
311B ARG* 1.3 81.7 - - - +
313B ALA* 1.3 95.7 + - + +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il