Contacts of the helix formed by residues 298 - 316 (chain B) in PDB entry 3ITX
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 GLU 298 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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255B LEU* 6.2 0.2 - - - +
284B ASP* 2.8 17.2 + - - +
285B SER 4.7 2.1 - - - +
286B LYS* 5.9 0.7 - - - -
297B ILE* 1.3 85.7 - - + +
299B PRO* 1.3 66.6 - - - +
300B TYR* 3.2 3.1 - - + +
301B ARG* 3.3 63.7 + - + +
302B LEU* 3.4 10.4 + - - +
297C ILE 5.0 1.6 - - - +
298C GLU* 3.4 46.9 - - + +
300C TYR* 5.2 1.1 - - + -
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Residues in contact with PRO 299 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
295B GLY* 3.6 27.7 - - - +
298B GLU* 1.3 87.8 - - - +
300B TYR* 1.3 60.2 + - - +
302B LEU* 3.3 6.2 + - + +
303B PHE* 3.1 20.4 + - - +
345B GLU* 3.9 15.7 - - - +
349B ALA* 5.3 1.6 - - - +
381B TYR* 3.2 26.8 - - + +
300C TYR* 3.7 26.7 - - + -
378C LYS* 4.3 5.2 - - - +
381C TYR* 3.8 18.4 - - + -
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Residues in contact with TYR 300 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
298B GLU* 3.2 1.2 - - + -
299B PRO* 1.3 80.2 - - + +
301B ARG* 1.3 60.9 + - - +
303B PHE* 3.0 25.5 + + - +
304B LEU* 2.9 55.1 + - + +
374B THR* 4.5 2.9 + - - -
377B LEU* 4.0 15.2 - - - +
378B LYS* 3.4 29.1 - - + +
381B TYR* 3.4 37.0 + + + -
296C ALA 3.6 21.1 + - - -
297C ILE 3.3 21.8 - - - +
298C GLU* 5.2 0.9 - - + -
299C PRO* 3.6 28.5 - - + -
187D PRO* 4.1 8.4 - - + +
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Residues in contact with ARG 301 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
255B LEU* 3.7 27.6 - - + +
262B THR 5.6 2.5 + - - -
264B ILE* 4.3 23.5 - - + +
265B GLU* 4.2 15.0 - - - +
284B ASP* 2.9 26.5 + - - -
285B SER* 3.1 24.5 + - - +
298B GLU* 3.3 47.6 + - - +
300B TYR* 1.3 77.7 - - - +
302B LEU* 1.3 63.7 + - - +
304B LEU* 3.2 13.2 + - - +
305B VAL* 3.0 28.6 + - + +
286C LYS* 5.6 8.1 - - - +
297C ILE 5.4 1.4 + - - -
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Residues in contact with LEU 302 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
255B LEU* 4.8 16.3 - - + +
280B PHE* 5.3 0.2 - - + -
282B PHE* 3.7 35.7 - - + -
283B ASN 5.8 0.4 - - - +
284B ASP* 6.4 0.7 - - - -
294B ALA* 5.2 1.6 - - + -
295B GLY* 4.0 14.1 - - - +
298B GLU 3.4 8.5 + - - +
299B PRO* 3.3 10.7 + - + +
300B TYR 3.2 0.4 - - - -
301B ARG* 1.3 79.4 - - - +
303B PHE* 1.3 63.0 + - - +
305B VAL* 3.3 9.5 + - + +
306B PHE* 3.1 25.2 + - + -
345B GLU* 3.8 35.9 - - + +
346B ILE* 3.8 19.7 - - + -
349B ALA* 3.7 10.3 - - + -
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Residues in contact with PHE 303 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
299B PRO 3.1 8.1 + - - +
300B TYR* 3.0 35.1 + + - +
302B LEU* 1.3 76.8 - - - +
304B LEU* 1.3 66.3 + - + +
306B PHE* 3.1 4.6 + - - +
307B ASN* 2.7 35.3 + - + +
349B ALA* 4.0 12.3 - - + +
352B GLN* 3.7 31.6 - - + +
353B ALA* 3.7 26.7 - - - -
356B VAL* 3.9 17.5 - - + -
377B LEU* 3.6 33.0 - - + -
381B TYR* 3.7 25.6 - + + -
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Residues in contact with LEU 304 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
265B GLU* 3.6 33.5 - - + +
300B TYR* 2.9 41.2 + - + +
301B ARG* 3.2 12.1 + - - +
303B PHE* 1.3 88.9 - - + +
305B VAL* 1.3 65.5 + - - +
307B ASN* 3.3 15.2 + - + +
308B GLU* 3.4 17.3 + - - +
377B LEU* 3.9 25.8 - - + -
297C ILE* 5.2 2.9 - - + +
187D PRO* 3.9 16.6 - - + -
228D TYR* 3.8 11.0 - - + +
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Residues in contact with VAL 305 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
255B LEU* 5.2 3.1 - - + -
264B ILE* 4.8 4.0 - - + -
265B GLU* 4.1 27.1 - - + +
268B VAL* 4.3 8.7 - - + +
280B PHE* 3.9 46.0 - - + -
282B PHE* 4.9 3.8 - - + -
301B ARG* 3.0 24.4 + - + +
302B LEU* 3.5 12.3 - - + +
303B PHE 3.2 0.2 - - - -
304B LEU* 1.3 75.8 - - - +
306B PHE* 1.3 64.4 + - - +
308B GLU* 3.1 15.6 + - - +
309B LEU* 3.1 24.3 + - + +
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Residues in contact with PHE 306 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50B PHE* 3.5 29.8 - + - -
282B PHE* 3.7 28.0 - + - -
302B LEU* 3.1 21.7 + - + +
303B PHE 3.1 7.6 + - - +
305B VAL* 1.3 76.2 - - + +
307B ASN* 1.3 58.6 + - - +
309B LEU* 3.6 21.9 - - + +
310B VAL* 2.8 34.5 + - - +
346B ILE* 3.4 38.8 - - + -
349B ALA* 3.4 34.1 - - + +
350B TYR* 3.8 26.2 - + + -
353B ALA* 3.8 3.8 - - + -
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Residues in contact with ASN 307 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303B PHE* 2.7 24.2 + - + +
304B LEU* 3.4 16.1 + - + +
305B VAL 3.1 0.2 - - - -
306B PHE* 1.3 73.6 - - - +
308B GLU* 1.3 72.4 + - - +
310B VAL 3.6 0.2 + - - -
311B ASP* 3.0 28.1 + - - +
353B ALA* 4.1 4.5 - - - +
356B VAL* 4.0 2.6 - - - +
358B ARG* 2.7 39.0 + - - +
361B LEU* 4.9 4.0 - - - +
377B LEU* 3.6 33.8 - - - +
188D GLY* 5.6 2.2 - - - +
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Residues in contact with GLU 308 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
265B GLU* 3.6 25.6 - - + +
268B VAL* 4.3 15.3 - - + -
269B ALA* 3.5 18.3 - - + +
272B ILE* 4.1 4.5 - - + +
304B LEU 3.4 11.6 + - - +
305B VAL 3.1 8.6 + - - +
307B ASN* 1.3 94.8 + - - +
309B LEU* 1.3 59.7 + - - +
311B ASP* 3.5 11.1 + - - +
312B ALA* 3.2 23.2 + - - +
315B ARG* 5.8 1.2 + - - -
190D SER 5.6 1.0 - - - +
191D ASN* 6.0 1.0 - - - -
192D PHE* 3.3 31.9 + - - +
193D THR* 5.3 1.4 + - - -
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Residues in contact with LEU 309 (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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50B PHE* 6.0 0.2 - - + -
268B VAL* 4.0 10.5 - - + -
272B ILE* 4.4 0.9 - - + -
277B LEU* 4.0 22.4 - - + -
280B PHE* 5.3 3.1 - - + -
282B PHE* 4.6 3.1 - - + -
305B VAL* 3.1 26.5 + - + +
306B PHE* 3.2 40.1 + - + +
308B GLU* 1.3 77.9 - - - +
310B VAL* 1.3 57.6 + - + +
312B ALA* 3.4 0.9 + - - -
313B GLU* 2.8 31.5 + - - +
320B PHE* 3.7 28.2 - - + -
324B HIS* 4.0 27.6 - - + +
350B TYR* 6.2 0.2 - - + -
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Residues in contact with VAL 310 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
306B PHE* 2.8 23.3 + - + +
309B LEU* 1.3 70.7 - - - +
311B ASP* 1.3 60.0 - - - +
313B GLU* 3.6 7.3 - - - +
314B ALA* 2.8 35.3 + - + +
350B TYR* 4.0 29.8 - - + -
353B ALA* 3.4 25.6 - - + +
354B LEU* 4.0 19.5 - - + -
358B ARG* 3.5 26.5 - - - +
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Residues in contact with ASP 311 (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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307B ASN* 3.0 20.1 + - - +
308B GLU* 3.6 14.2 - - - +
310B VAL* 1.3 77.8 - - - +
312B ALA* 1.3 52.7 + - - +
314B ALA* 3.9 2.3 - - - +
315B ARG* 2.7 82.3 + - - +
358B ARG* 4.1 26.5 + - - +
191D ASN* 4.1 14.3 + - - -
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Residues in contact with ALA 312 (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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272B ILE* 3.9 27.6 - - + -
308B GLU 3.2 14.0 + - - +
309B LEU 3.7 3.4 - - - +
311B ASP* 1.3 78.8 + - - +
313B GLU* 1.3 63.3 + - - +
315B ARG* 3.9 4.0 - - - +
316B GLY 2.8 33.3 + - - +
317B VAL* 3.4 22.2 - - + -
320B PHE* 4.1 11.2 - - + -
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Residues in contact with GLU 313 (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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46B LYS* 4.8 7.3 + - - +
50B PHE* 5.2 4.5 - - - -
309B LEU* 2.8 19.7 + - - +
310B VAL* 3.2 8.1 + - + +
312B ALA* 1.3 77.5 - - - +
314B ALA* 1.3 61.5 + - + +
316B GLY* 4.0 5.6 + - - +
320B PHE* 3.7 17.7 - - + -
350B TYR* 2.8 42.2 + - - -
354B LEU* 4.2 9.0 - - - +
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Residues in contact with ALA 314 (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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46B LYS* 6.3 0.4 - - - +
310B VAL* 2.8 23.2 + - + +
311B ASP* 3.9 3.4 - - - +
313B GLU* 1.3 77.0 - - + +
315B ARG* 1.3 59.6 + - - +
316B GLY* 2.9 10.6 + - - -
358B ARG* 5.6 10.1 - - + -
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Residues in contact with ARG 315 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272B ILE* 4.5 13.9 - - - +
273B GLN* 5.2 3.6 - - - +
308B GLU* 5.8 1.4 + - - -
311B ASP* 2.7 58.0 + - - +
312B ALA* 4.2 3.3 - - - +
314B ALA* 1.3 71.5 - - - +
316B GLY* 1.3 55.8 + - - +
317B VAL* 3.1 33.5 + - + +
191D ASN* 4.1 12.5 + - - +
193D THR* 3.7 41.2 + - - +
194D ARG* 5.4 3.0 - - - +
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Residues in contact with GLY 316 (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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312B ALA 2.8 16.8 + - - +
313B GLU* 4.0 5.7 + - - +
314B ALA 2.9 8.3 + - - -
315B ARG* 1.3 75.9 - - - +
317B VAL* 1.3 72.4 + - - +
320B PHE* 4.4 5.9 - - - +
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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