Contacts of the helix formed by residues 257 - 274 (chain B) in PDB entry 3GA5
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 ASP 257 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
255B LEU* 3.9 17.8 + - + -
256B ASN* 1.3 71.1 + - - +
258B ALA* 1.3 61.0 + - - +
259B ASN* 3.3 10.6 + - - +
260B ASN* 2.7 46.9 + - - +
261B GLN* 3.1 28.4 + - - +
293B VAL* 3.5 20.4 + - + +
294B PRO* 4.1 12.3 + - - +
295B TYR* 5.3 0.2 - - - -
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Residues in contact with ALA 258 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16B PHE* 3.7 24.7 - - + -
19B VAL* 3.6 31.9 - - + +
20B VAL* 3.8 18.6 - - + +
23B ALA* 5.1 0.9 - - - -
255B LEU* 5.7 0.2 - - - +
256B ASN 2.9 7.6 + - - +
257B ASP* 1.3 70.1 + - - +
259B ASN* 1.3 65.6 + - - +
261B GLN* 3.4 1.2 + - - +
262B ALA* 2.9 27.9 + - - +
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Residues in contact with ASN 259 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19B VAL* 5.5 4.1 - - - +
23B ALA* 3.9 20.8 - - - +
257B ASP* 3.3 7.8 + - - +
258B ALA* 1.3 80.7 - - - +
260B ASN* 1.3 62.8 + - - +
262B ALA* 3.5 2.4 + - - +
263B LYS* 2.9 27.9 + - - +
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Residues in contact with ASN 260 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
257B ASP* 2.7 36.7 + - - +
259B ASN* 1.3 77.7 - - - +
261B GLN* 1.3 61.1 + - - +
263B LYS* 4.2 12.1 - - - +
264B ALA* 2.9 26.9 + - - +
284B TRP* 3.4 27.4 - - + -
293B VAL* 3.9 13.6 - - + +
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Residues in contact with GLN 261 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16B PHE* 4.1 4.8 - - - -
20B VAL* 5.1 9.4 - - + +
90B PHE* 6.0 2.5 - - + -
91B ASN* 4.9 2.8 - - - +
108B VAL* 3.6 15.2 - - + +
109B GLY* 3.8 10.8 - - - +
110B THR* 3.5 14.2 - - - +
256B ASN* 2.7 29.7 + - - -
257B ASP* 3.1 25.0 + - - +
258B ALA* 4.0 4.5 - - - +
260B ASN* 1.3 74.9 - - - +
262B ALA* 1.3 60.8 + - - +
265B THR* 2.8 30.9 + - - +
293B VAL* 3.8 19.7 - - + +
401B RGG 2.7 30.9 + - - -
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Residues in contact with ALA 262 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20B VAL* 3.7 9.8 - - + +
23B ALA* 3.5 26.5 - - + -
24B ILE* 3.5 32.0 - - + +
27B ASP* 4.9 1.3 - - - -
258B ALA 2.9 19.8 + - - +
259B ASN 3.7 1.8 - - - +
261B GLN* 1.3 72.5 - - - +
263B LYS* 1.3 66.5 + - - +
265B THR* 3.4 2.3 + - - -
266B PHE* 3.0 25.7 + - - +
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Residues in contact with LYS 263 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27B ASP* 3.9 23.4 + - - +
259B ASN 2.9 18.3 + - - +
260B ASN* 3.3 16.1 + - - +
262B ALA* 1.3 77.1 - - - +
264B ALA* 1.3 57.0 + - - +
266B PHE* 3.8 0.7 - - - +
267B ASP* 2.8 55.5 + - - +
284B TRP* 3.9 14.6 - - + -
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Residues in contact with ALA 264 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108B VAL* 3.7 24.9 - - + -
260B ASN 2.9 17.0 + - - +
263B LYS* 1.3 73.1 - - - +
265B THR* 1.3 66.7 + - - +
268B LEU* 2.9 31.0 + - + +
284B TRP* 3.4 36.3 - - + +
291B VAL* 4.2 7.0 - - + -
293B VAL* 5.3 0.2 - - + -
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Residues in contact with THR 265 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24B ILE* 3.9 18.2 - - + -
64B ALA* 3.9 15.7 - - + -
88B VAL* 4.2 8.7 - - + +
90B PHE* 3.3 47.9 - - + +
108B VAL* 3.5 14.8 - - - +
261B GLN 2.8 22.4 + - - -
262B ALA 3.7 3.4 - - - -
264B ALA* 1.3 77.2 - - - +
266B PHE* 1.3 58.4 + - - +
268B LEU* 4.1 0.7 - - - +
269B ALA* 3.0 30.5 + - - +
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Residues in contact with PHE 266 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5B ILE* 5.2 2.9 - - + -
24B ILE* 4.1 15.7 - - + -
27B ASP* 3.6 45.8 - - + +
28B GLY* 3.6 23.1 - - - -
31B ALA* 4.1 13.7 - - + -
34B VAL* 4.0 18.6 - - + -
36B LEU* 4.0 14.6 - - + -
262B ALA 3.0 17.0 + - - +
263B LYS 3.8 2.5 - - - +
265B THR* 1.3 76.0 - - - +
267B ASP* 1.3 75.6 + - - +
269B ALA* 3.3 4.2 + - + +
270B LYS* 2.9 47.3 + - + +
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Residues in contact with ASP 267 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27B ASP* 4.6 1.4 - - - +
263B LYS* 2.8 48.0 + - - +
264B ALA 3.9 0.4 - - - +
266B PHE* 1.3 85.8 - - - +
268B LEU* 1.3 58.2 + - + +
270B LYS* 3.8 4.2 - - - +
271B ASN* 3.0 35.8 + - - -
282B THR* 4.1 19.9 - - + +
284B TRP* 2.9 31.1 + - + +
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Residues in contact with LEU 268 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88B VAL* 4.2 11.7 - - + -
106B TYR* 4.4 20.0 - - + -
107B TYR 5.3 0.9 - - - +
108B VAL* 3.9 24.0 - - + -
264B ALA* 2.9 20.7 + - + +
265B THR 4.2 1.6 - - - +
267B ASP* 1.3 76.0 - - - +
269B ALA* 1.3 65.7 + - - +
271B ASN* 3.4 1.6 + - - +
272B LEU* 3.0 30.3 + - + +
278B ALA* 3.4 26.7 - - + +
279B ALA* 4.9 0.2 - - - -
284B TRP* 3.9 27.8 - - + -
286B ILE* 3.8 26.7 - - + -
289B LYS 5.6 0.2 - - - +
291B VAL* 4.1 9.4 - - + -
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Residues in contact with ALA 269 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5B ILE* 4.1 24.9 - - + -
62B ALA* 3.5 10.7 - - + +
63B LEU 4.9 0.2 - - - +
64B ALA* 4.5 9.6 - - + -
88B VAL* 3.7 20.6 - - + +
265B THR 3.0 20.3 + - - +
266B PHE* 3.9 4.5 - - + +
268B LEU* 1.3 75.8 - - - +
270B LYS* 1.3 56.8 + - - +
272B LEU* 3.4 1.4 + - - -
273B ALA* 2.9 31.0 + - - +
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Residues in contact with LYS 270 (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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3B THR* 5.7 1.1 - - + -
5B ILE* 3.8 14.6 - - + +
31B ALA* 4.4 7.0 - - - -
33B ASP* 3.1 26.0 + - - -
34B VAL* 3.6 21.5 - - + -
266B PHE* 2.9 39.7 + - + +
267B ASP* 3.8 5.4 - - - +
269B ALA* 1.3 75.3 - - - +
271B ASN* 1.3 67.0 + - - +
273B ALA* 3.4 3.0 + - - +
274B GLU* 2.8 54.0 + - - +
276B LYS* 5.5 1.0 - - - +
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Residues in contact with ASN 271 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
267B ASP* 3.0 19.4 + - - +
268B LEU 3.8 1.3 - - - +
270B LYS* 1.3 79.6 - - - +
272B LEU* 1.3 60.3 + - - +
274B GLU* 3.1 15.8 + - - +
276B LYS* 2.8 37.6 + - + +
277B GLY 3.3 19.1 - - - +
278B ALA* 3.1 23.2 + - - +
279B ALA 3.8 0.8 - - - -
280B ASP* 3.0 38.2 + - - +
282B THR* 4.1 6.3 - - - +
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Residues in contact with LEU 272 (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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103A ASP* 3.8 21.6 - - + +
61B LYS 4.5 0.5 - - - +
62B ALA* 5.0 0.2 - - + -
86B PRO* 3.7 34.5 - - + +
88B VAL* 3.9 17.7 - - + -
104B LYS* 5.4 2.9 - - + -
106B TYR* 3.6 44.2 - - + +
268B LEU* 3.0 22.2 + - + +
269B ALA* 3.9 3.4 - - - +
271B ASN* 1.3 76.1 - - - +
273B ALA* 1.3 59.1 + - - +
275B GLY* 3.0 17.2 + - - -
276B LYS 3.8 16.4 - - - +
278B ALA* 3.9 19.5 - - + +
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Residues in contact with ALA 273 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3B THR* 3.9 18.6 - - + -
5B ILE* 4.3 4.9 - - + -
61B LYS* 3.5 47.0 - - + +
62B ALA* 3.7 13.6 - - + +
269B ALA 2.9 19.0 + - - +
270B LYS 3.5 6.7 - - - +
272B LEU* 1.3 77.2 - - - +
274B GLU* 1.3 57.5 + - - +
275B GLY 3.2 1.1 + - - -
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Residues in contact with GLU 274 (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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81A ARG* 4.6 4.2 + - - -
3B THR* 4.7 14.5 + - + +
33B ASP* 3.5 9.7 - - - +
34B VAL* 5.3 0.7 - - - +
270B LYS* 2.8 49.2 + - + +
271B ASN* 3.1 13.1 + - - +
273B ALA* 1.3 76.8 - - + +
275B GLY* 1.3 61.5 + - - +
276B LYS* 2.9 45.0 + - - +
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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
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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