Contacts of the helix formed by residues 301 - 323 (chain B) in PDB entry 1GPU
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 ILE 301 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45B TRP* 3.4 30.7 - - + +
46B SER* 3.8 9.9 - - - +
48B MET 5.0 4.6 - - - +
50B MET* 3.4 29.4 - - + +
52B PRO* 4.3 15.5 - - + -
81B THR* 3.6 22.9 - - + +
297B TYR* 2.8 42.0 + - + +
299B LYS 3.6 0.4 - - - -
300B THR* 1.3 85.5 - - - +
302B LEU* 1.3 59.7 + - - +
304B PRO* 3.5 4.7 - - - +
305B GLY* 2.9 27.5 + - - -
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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
----------------------------------------------------------
52B PRO* 3.6 33.7 - - + +
53B THR* 3.5 24.0 - - - +
81B THR 4.1 6.3 - - - +
82B GLY* 4.3 17.9 - - - +
297B TYR 3.0 13.6 + - - +
298B GLN* 3.2 39.5 - - - +
301B ILE* 1.3 72.2 - - - +
303B LYS* 1.3 61.7 + - - +
305B GLY* 3.1 1.4 + - - -
306B VAL* 2.9 38.5 + - + +
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Residues in contact with LYS 303 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
298B GLN* 2.9 54.6 + - + +
299B LYS* 4.8 4.9 - - - +
302B LEU* 1.3 73.5 - - + +
304B PRO* 1.3 65.1 - - + +
306B VAL* 3.3 8.4 + - - +
307B GLU* 3.0 23.7 + - - +
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Residues in contact with PRO 304 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
298B GLN 3.7 0.4 - - - +
299B LYS 3.1 28.7 - - - +
300B THR* 3.7 14.1 - - - +
301B ILE 3.5 14.8 - - - +
303B LYS* 1.3 93.4 - - + +
305B GLY* 1.3 55.5 + - - +
307B GLU* 3.4 6.3 + - + +
308B ALA* 2.9 29.3 + - - +
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Residues in contact with GLY 305 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49B ARG* 5.4 1.8 - - - -
50B MET 3.0 31.1 - - - +
51B ASN* 3.9 6.4 - - - +
57B TRP* 4.5 1.6 - - - -
301B ILE 2.9 15.3 + - - -
302B LEU 3.6 0.9 - - - -
304B PRO* 1.3 75.1 - - - +
306B VAL* 1.3 64.1 + - - +
308B ALA* 3.2 7.0 + - - +
309B ASN* 2.9 24.6 + - - +
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Residues in contact with VAL 306 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51B ASN* 3.5 28.5 - - - +
53B THR* 3.9 14.8 - - + +
302B LEU* 2.9 26.6 + - + +
303B LYS* 3.7 7.6 - - - +
305B GLY* 1.3 76.1 - - - +
307B GLU* 1.3 59.6 + - - +
309B ASN* 3.4 3.8 + - - +
310B ASN* 2.9 27.2 + - + +
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Residues in contact with GLU 307 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303B LYS 3.0 17.1 + - - +
304B PRO* 3.7 6.5 - - + +
305B GLY 3.2 0.2 - - - -
306B VAL* 1.3 76.7 - - - +
308B ALA* 1.3 61.3 + - - +
310B ASN* 3.1 22.5 + - - +
311B LYS* 2.8 57.9 + - + +
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Residues in contact with ALA 308 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49B ARG* 3.7 37.0 - - + +
57B TRP* 3.9 7.0 - - + -
304B PRO 2.9 17.4 + - - +
305B GLY 3.2 5.1 + - - +
307B GLU* 1.3 76.2 - - - +
309B ASN* 1.3 62.9 + - - +
311B LYS* 3.3 11.9 + - - +
312B TRP* 2.9 23.4 + - - +
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Residues in contact with ASN 309 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51B ASN* 3.0 25.6 - - + +
54B ASN* 3.0 28.1 + - - +
57B TRP* 3.4 45.3 + - + +
305B GLY 2.9 16.8 + - - +
306B VAL 3.6 5.4 - - - +
308B ALA* 1.3 75.8 - - - +
310B ASN* 1.3 58.0 + - - +
312B TRP* 3.3 1.6 + - - +
313B ASN* 2.9 43.6 + - - +
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Residues in contact with ASN 310 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
306B VAL* 2.9 17.9 + - + +
307B GLU* 3.1 32.9 + - - +
309B ASN* 1.3 74.0 - - - +
311B LYS* 1.3 65.3 + - - +
313B ASN* 3.2 11.2 + - - +
314B LYS* 3.0 21.8 + - - +
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Residues in contact with LYS 311 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
307B GLU* 2.8 50.1 + - + +
308B ALA* 3.7 7.6 - - - +
310B ASN* 1.3 73.8 - - - +
312B TRP* 1.3 58.1 - - - +
314B LYS* 3.2 13.9 + - + +
315B LEU* 2.9 27.9 + - - +
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Residues in contact with TRP 312 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57B TRP* 3.4 24.7 - + + +
58B ILE* 3.5 31.2 - - + -
59B ASN* 3.6 19.8 - - + +
145B THR 4.8 2.9 - - - -
146B LEU* 2.8 47.6 + - + +
308B ALA 2.9 14.3 + - - +
309B ASN 3.5 7.9 - - - +
311B LYS* 1.3 74.2 - - - +
313B ASN* 1.3 83.2 + - - +
315B LEU* 3.1 12.2 + - + +
316B PHE* 2.8 61.1 + + + -
330B LEU* 5.2 3.8 - - + -
334B LEU* 4.1 13.0 - - + -
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Residues in contact with ASN 313 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57B TRP* 5.4 0.2 - - - -
309B ASN* 2.9 31.0 + - - +
310B ASN* 3.2 12.9 + - - +
312B TRP* 1.3 101.9 - - - +
314B LYS* 1.3 58.9 + - - +
316B PHE* 3.9 4.5 - - - +
317B SER* 3.0 29.6 + - - -
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Residues in contact with LYS 314 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
310B ASN* 3.0 13.4 + - - +
311B LYS* 3.4 14.4 - - + +
312B TRP 3.2 0.2 - - - -
313B ASN* 1.3 77.2 - - - +
315B LEU* 1.3 63.5 + - - +
317B SER* 3.3 7.7 + - - -
318B GLU* 3.1 26.9 + - - +
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Residues in contact with LEU 315 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143B GLY 3.7 13.9 - - - +
144B PHE* 3.4 31.6 - - + -
145B THR* 3.8 32.3 - - - +
146B LEU* 4.1 12.3 - - + -
311B LYS 2.9 14.1 + - - +
312B TRP* 3.5 15.3 - - + +
314B LYS* 1.3 78.9 - - - +
316B PHE* 1.3 56.1 + - - +
318B GLU* 3.4 6.7 + - + +
319B TYR* 2.9 26.2 + - - +
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Residues in contact with PHE 316 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146B LEU* 4.1 12.7 - - + +
312B TRP* 2.8 45.3 + + + +
313B ASN* 3.9 4.7 - - - +
315B LEU* 1.3 74.0 - - - +
317B SER* 1.3 66.0 + - - +
319B TYR* 3.2 20.4 + + - -
320B GLN* 3.0 57.1 + - + +
327B GLY 3.9 1.1 - - - -
330B LEU* 3.7 27.6 - - + -
331B ALA* 3.8 27.1 - - + -
334B LEU* 3.9 15.5 - - + -
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Residues in contact with SER 317 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
313B ASN 3.0 18.7 + - - -
314B LYS* 3.3 8.9 + - - -
316B PHE* 1.3 77.5 - - - +
318B GLU* 1.3 61.8 + - - +
320B GLN* 3.4 20.0 + - - +
321B LYS* 3.4 30.0 + - - +
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Residues in contact with GLU 318 (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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144B PHE* 3.9 19.3 - - + -
314B LYS* 3.1 14.9 + - - +
315B LEU* 3.7 9.9 - - + +
317B SER* 1.3 76.4 - - - +
319B TYR* 1.3 62.0 + - - +
321B LYS* 3.0 25.6 + - - +
322B LYS* 2.9 37.5 + - + +
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Residues in contact with TYR 319 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139B TYR* 2.8 39.5 + - - +
141B LYS* 4.0 7.2 - - + -
144B PHE* 3.6 28.5 - - + -
146B LEU* 3.6 28.5 - - + -
315B LEU 2.9 15.2 + - - +
316B PHE* 3.3 21.1 - + + +
318B GLU* 1.3 77.8 - - - +
320B GLN* 1.3 55.8 + - - +
322B LYS* 3.2 1.2 + - - +
323B PHE* 2.7 54.4 + + + +
326B LEU* 3.5 26.5 - - + +
327B GLY* 3.6 28.9 - - - -
330B LEU* 5.0 2.2 - - + -
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Residues in contact with GLN 320 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
316B PHE* 3.0 50.1 + - + +
317B SER* 3.6 13.4 - - - +
318B GLU 3.2 0.2 - - - -
319B TYR* 1.3 76.9 - - - +
321B LYS* 1.3 61.2 + - + +
323B PHE 4.1 6.1 - - - -
324B PRO* 3.4 23.2 - - - +
327B GLY* 3.8 22.4 + - - +
328B ALA* 5.2 1.8 - - - +
331B ALA* 3.6 23.2 - - - +
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Residues in contact with LYS 321 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
317B SER* 3.4 27.6 + - - +
318B GLU* 3.0 30.6 + - - +
320B GLN* 1.3 75.3 - - + +
322B LYS* 1.3 65.0 + - - +
323B PHE 3.7 0.2 + - - -
324B PRO* 3.8 13.4 - - - +
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Residues in contact with LYS 322 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142B PRO 5.8 0.4 - - - -
144B PHE* 3.6 35.4 - - + -
318B GLU* 2.9 24.4 + - + +
319B TYR 3.6 3.1 - - - +
321B LYS* 1.3 78.6 - - - +
323B PHE* 1.3 94.1 + - + +
324B PRO* 3.4 6.9 - - - +
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Residues in contact with PHE 323 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141B LYS* 3.6 46.4 - - + -
142B PRO* 5.4 3.4 - - + -
144B PHE* 3.8 12.1 - + - -
319B TYR* 2.7 37.1 + + + +
320B GLN 3.7 3.3 - - - +
322B LYS* 1.3 114.9 - - + +
324B PRO* 1.3 56.4 - - - +
325B GLU 3.3 2.2 - - - -
326B LEU* 4.2 19.5 - - + +
327B GLY* 2.7 37.0 + - - +
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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) + - + + + + + -
------------------------------------------------------------
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