Contacts of the helix formed by residues 14 - 31 (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 14 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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10B TYR* 2.6 40.5 + - + +
11B LYS* 3.2 19.2 + - + +
12B TYR 3.2 2.5 - - - +
13B ASP* 1.3 77.5 + - - +
15B ASN* 1.3 66.1 + - - +
16B PHE 3.3 2.8 + - - -
17B MET* 2.9 23.6 + - + +
18B SER* 3.0 23.8 + - - -
183B TRP* 3.9 10.9 - - - +
211B ASN* 5.3 0.6 + - - -
401B RGG 2.6 35.7 + - - -
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Residues in contact with ASN 15 (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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13B ASP 3.5 8.9 + - - +
14B ASP* 1.3 72.0 + - - +
16B PHE* 1.3 62.6 + - - +
18B SER* 2.7 25.5 + - - -
19B VAL* 3.4 8.8 + - - +
183B TRP 4.9 1.4 + - - +
184B ASP* 5.8 0.7 - - - -
185B THR* 4.4 7.5 + - - -
213B ALA* 3.6 24.1 - - + +
216B MET* 4.3 16.4 - - - +
238B LEU* 3.7 28.4 - - + +
240B GLU* 5.1 5.9 + - - -
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Residues in contact with PHE 16 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14B ASP* 3.3 1.8 + - - -
15B ASN* 1.3 80.0 - - - +
17B MET* 1.3 58.9 + - - +
19B VAL* 2.9 23.7 + - + +
20B VAL* 3.0 26.0 + - + -
91B ASN* 4.0 6.3 - - - -
236B ASP* 3.6 33.4 - - + +
238B LEU* 4.1 13.2 - - + +
256B ASN* 3.1 59.0 - - + -
258B ALA* 3.7 26.0 - - + -
261B GLN* 4.1 2.7 - - - -
401B RGG 3.4 41.6 + - - +
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Residues in contact with MET 17 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9B ILE* 3.7 31.1 - - + +
10B TYR* 4.4 4.3 - - + -
11B LYS 4.8 0.9 - - - +
14B ASP* 2.9 29.2 + - + +
16B PHE* 1.3 73.9 - - - +
18B SER* 1.3 55.6 + - - +
20B VAL* 3.7 19.3 - - + -
21B ARG* 2.7 34.8 + - - +
66B ASN* 3.5 21.1 - - - +
90B PHE* 3.6 25.6 - - + -
91B ASN* 3.3 46.0 - - - +
401B RGG 4.2 2.7 - - - +
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Residues in contact with SER 18 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12B TYR* 4.1 14.3 + - - +
14B ASP 3.0 13.9 + - - -
15B ASN* 2.7 22.0 + - - -
16B PHE 3.1 0.2 - - - -
17B MET* 1.3 74.4 - - - +
19B VAL* 1.3 61.4 + - - +
21B ARG* 3.7 14.0 - - - +
22B LYS* 2.9 50.4 + - - +
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Residues in contact with VAL 19 (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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15B ASN 3.6 14.1 - - - +
16B PHE* 2.9 9.8 + - + +
18B SER* 1.3 79.5 + - - +
20B VAL* 1.3 61.8 + - - +
22B LYS* 4.0 5.4 - - - +
23B ALA* 3.1 24.2 + - + +
238B LEU* 4.4 17.5 - - + -
239B PRO* 5.5 7.4 - - + -
258B ALA* 3.6 22.0 - - + -
259B ASN* 5.5 5.4 - - - +
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Residues in contact with VAL 20 (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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16B PHE* 3.0 40.3 + - + +
17B MET* 3.8 17.9 - - + +
19B VAL* 1.3 75.0 - - - +
21B ARG* 1.3 65.2 + - - +
23B ALA 3.2 1.4 + - - -
24B ILE* 3.0 30.5 + - + +
90B PHE* 3.9 31.2 - - + -
91B ASN* 5.4 0.9 - - + +
258B ALA* 3.8 19.1 - - + +
261B GLN* 5.1 7.9 - - + +
262B ALA* 3.7 15.9 - - + +
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Residues in contact with ARG 21 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9B ILE* 3.8 20.4 - - + -
12B TYR* 3.4 57.6 + - - +
17B MET 2.7 22.9 + - - +
18B SER* 3.7 12.5 - - - +
20B VAL* 1.3 73.6 - - - +
22B LYS* 1.3 87.7 + - - +
24B ILE* 3.1 8.0 + - - +
25B GLU* 2.8 70.0 + - - +
38B MET* 3.9 10.1 - - + -
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Residues in contact with LYS 22 (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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18B SER* 2.9 30.2 + - - +
19B VAL* 4.0 4.7 - - - +
21B ARG* 1.3 106.7 - - - +
23B ALA* 1.3 57.6 + - - +
25B GLU* 3.3 7.4 + - - +
26B LYS* 3.0 27.2 + - - +
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Residues in contact with ALA 23 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19B VAL* 3.1 17.9 + - + +
22B LYS* 1.3 73.8 - - - +
24B ILE* 1.3 65.7 + - - +
26B LYS* 3.4 12.5 + - + +
27B ASP* 3.3 23.4 + - - +
258B ALA 4.7 1.1 - - - +
259B ASN* 3.9 25.4 - - - +
262B ALA* 3.5 21.7 - - + +
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Residues in contact with ILE 24 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7B VAL* 4.9 17.9 - - + -
9B ILE* 5.3 0.7 - - + -
20B VAL* 3.0 21.8 + - + +
21B ARG* 3.5 9.4 - - - +
23B ALA* 1.3 77.2 - - - +
25B GLU* 1.3 63.0 + - - +
27B ASP* 3.1 17.5 + - - +
28B GLY 3.1 9.2 + - - -
36B LEU* 3.7 21.4 - - + +
38B MET* 5.2 2.7 - - + -
64B ALA* 5.8 0.4 - - + -
90B PHE* 3.6 35.9 - - + -
262B ALA* 3.5 22.9 - - + +
265B THR* 3.9 19.5 - - + -
266B PHE* 4.1 11.6 - - + -
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Residues in contact with GLU 25 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12B TYR* 4.1 2.4 + - - -
21B ARG* 2.8 50.6 + - - +
22B LYS* 3.8 7.2 - - - +
24B ILE* 1.3 74.6 - - - +
26B LYS* 1.3 58.3 + - - +
28B GLY* 3.1 1.2 + - - -
29B LYS* 2.9 53.3 + - - +
36B LEU* 4.1 7.6 - - + +
38B MET* 3.3 45.9 - - + +
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Residues in contact with LYS 26 (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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22B LYS 3.0 14.0 + - - +
23B ALA* 3.4 15.0 - - + +
25B GLU* 1.3 76.5 - - - +
27B ASP* 1.3 65.7 + - - +
29B LYS* 3.3 13.1 + - + +
30B SER* 3.1 31.2 + - - +
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Residues in contact with ASP 27 (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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23B ALA 3.3 9.2 + - - +
24B ILE 3.1 9.9 + - - +
26B LYS* 1.3 83.5 - - - +
28B GLY* 1.3 61.7 + - - +
30B SER* 3.2 14.7 + - - -
31B ALA* 3.2 15.9 + - - +
262B ALA 4.6 0.3 - - - +
263B LYS* 3.9 30.0 + - - +
266B PHE* 3.6 42.0 - - + +
267B ASP* 4.6 1.4 - - - +
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Residues in contact with GLY 28 (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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24B ILE 3.1 10.3 + - - -
25B GLU 3.1 3.5 + - - -
27B ASP* 1.3 76.1 - - - +
29B LYS* 1.3 57.5 + - - +
30B SER 3.3 0.2 + - - -
31B ALA 3.3 5.9 - - - +
34B VAL* 3.8 5.2 - - - +
36B LEU* 4.0 17.5 - - - -
266B PHE* 3.6 17.4 - - - -
701B NA 2.4 30.5 - - - -
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Residues in contact with LYS 29 (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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25B GLU* 2.9 41.0 + - - +
26B LYS* 3.6 10.2 - - + +
27B ASP 3.3 0.2 - - - -
28B GLY* 1.3 76.3 - - - +
30B SER* 1.3 60.3 + - - +
31B ALA 3.6 2.4 + - - -
32B PRO* 5.1 1.2 - - - +
701B NA 4.3 2.0 - - - -
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Residues in contact with SER 30 (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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26B LYS* 3.1 21.2 + - - +
27B ASP* 3.2 8.5 + - - -
28B GLY 3.2 0.6 - - - -
29B LYS* 1.3 76.2 - - - +
31B ALA* 1.3 59.4 + - - +
32B PRO* 3.4 10.4 - - - +
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Residues in contact with ALA 31 (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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27B ASP 3.2 14.7 + - - +
28B GLY 3.3 1.4 + - - +
29B LYS 4.7 0.7 - - - -
30B SER* 1.3 77.8 - - - +
32B PRO* 1.3 64.1 - - - +
33B ASP* 3.1 12.8 - - - +
34B VAL* 3.1 21.1 + - + -
266B PHE* 4.1 11.2 - - + -
270B LYS* 4.4 6.5 - - - -
701B NA 2.3 27.7 - - - -
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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
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Atomic class I II III IV V VI VII VIII
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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