Contacts of the helix formed by residues 25 - 38 (chain B) in PDB entry 4GSW
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 SER 25 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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31A ALA 4.5 0.3 + - - -
34A GLN* 2.9 34.0 + - - -
35A GLU* 2.9 22.6 + - - +
23B ASN 3.4 2.7 + - - -
24B ASP* 1.3 76.1 - - - +
26B ILE* 1.3 65.1 + - - +
27B ASP* 3.2 6.6 - - - +
28B ALA* 3.0 26.5 + - - +
29B ILE* 3.3 13.2 + - - +
56B GLY 5.1 0.2 - - - -
57B LYS 3.2 12.3 - - - -
58B THR* 4.1 4.7 - - - +
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Residues in contact with ILE 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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25B SER* 1.3 72.0 - - - +
27B ASP* 1.3 53.3 + - - +
29B ILE* 2.9 11.7 + - + +
30B LYS* 2.8 42.5 + - - +
46B LEU* 4.3 16.4 - - + -
53B LEU* 4.0 44.4 - - + +
54B GLU 3.4 26.7 - - - +
55B GLU* 5.0 1.3 - - - +
57B LYS* 2.8 25.3 + - + +
58B THR 4.2 10.8 - - - +
59B LEU* 4.0 24.5 - - + -
62B TYR* 4.3 5.8 - - + -
70B LEU* 6.1 0.2 - - + -
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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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31A ALA* 3.6 14.5 - - + +
34A GLN* 3.6 13.4 - - + +
41A PRO* 3.4 15.5 - - + +
25B SER* 3.2 11.9 + - - +
26B ILE* 1.3 74.7 + - - +
28B ALA* 1.3 55.9 + - - +
30B LYS* 3.4 10.7 + - - +
31B ALA* 2.9 29.1 + - - +
41B PRO* 5.5 2.2 - - - +
55B GLU* 2.6 38.2 - - - +
56B GLY* 2.9 24.4 + - - -
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Residues in contact with ALA 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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31A ALA* 3.9 13.2 - - + +
32A LYS* 6.4 1.1 - - + -
35A GLU* 3.4 29.6 - - - +
24B ASP* 4.2 13.5 - - - +
25B SER* 3.0 14.9 + - - +
27B ASP* 1.3 74.3 - - - +
29B ILE* 1.3 64.6 + - + +
31B ALA* 3.4 2.8 + - - +
32B LYS* 3.1 33.0 + - - +
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Residues in contact with ILE 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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6B ILE* 4.6 2.2 - - + -
8B VAL* 5.0 0.4 - - + -
18B LEU* 3.8 16.8 - - + -
20B VAL* 3.4 34.8 - - + -
24B ASP* 4.3 9.9 - - + +
25B SER 3.5 14.6 - - - +
26B ILE* 2.9 10.6 + - + +
28B ALA* 1.3 77.6 - - + +
30B LYS* 1.3 65.4 + - - +
31B ALA 3.1 0.2 - - - -
32B LYS* 3.2 9.4 + - + +
33B ILE* 3.0 27.2 + - + +
46B LEU* 4.0 20.4 - - + -
59B LEU* 3.8 24.7 - - + -
70B LEU* 4.2 14.8 - - + -
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Residues in contact with LYS 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 ILE* 2.8 26.9 + - + +
27B ASP* 3.4 11.9 + - - +
29B ILE* 1.3 76.9 - - - +
31B ALA* 1.3 52.7 + - - +
33B ILE* 3.2 1.0 + - - -
34B GLN* 2.7 30.7 + - - +
41B PRO* 3.0 37.2 + - + +
42B ASP* 4.8 4.2 + - - +
44B GLN* 2.8 62.2 + - - +
46B LEU* 3.7 19.7 - - + +
53B LEU 5.1 6.8 + - - -
55B GLU* 6.1 4.5 - - - +
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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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25A SER* 4.8 0.2 + - - -
27A ASP* 3.7 11.2 - - + +
28A ALA* 3.7 31.6 - - + +
31A ALA* 4.0 5.2 - - + -
27B ASP 2.9 17.9 + - - +
28B ALA* 3.7 5.8 - - - +
29B ILE 3.1 0.2 - - - -
30B LYS* 1.3 78.9 - - - +
32B LYS* 1.3 57.8 + - + +
34B GLN* 3.2 9.7 + - - +
35B GLU* 3.0 33.7 + - - +
41B PRO* 4.8 4.9 - - + +
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Residues in contact with LYS 32 (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 LEU* 4.3 25.3 - - + +
19B GLU 2.9 28.5 + - - +
20B VAL* 4.0 11.9 - - + +
21B GLU* 6.1 0.4 - - - +
24B ASP* 3.6 21.4 + - - -
28B ALA* 3.1 21.2 + - - +
29B ILE* 3.6 8.0 - - + +
31B ALA* 1.3 74.4 - - + +
33B ILE* 1.3 64.1 + - - +
35B GLU* 3.4 14.7 + - - +
36B LYS* 3.2 24.4 + - - +
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Residues in contact with ILE 33 (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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8B VAL* 4.2 18.8 - - + -
16B ILE* 4.9 6.7 - - + -
18B LEU* 4.3 11.4 - - + -
29B ILE* 3.0 21.4 + - + +
30B LYS 3.5 1.3 - - - +
32B LYS* 1.3 74.2 - - - +
34B GLN* 1.3 67.0 + - - +
36B LYS* 4.5 4.7 - - - +
37B GLU* 2.9 40.0 + - + +
39B ILE* 4.8 2.5 - - + -
44B GLN* 3.5 32.5 - - + +
46B LEU* 3.7 31.2 - - + -
72B LEU* 3.9 21.1 - - + -
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Residues in contact with GLN 34 (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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25A SER* 2.9 33.7 + - - -
27A ASP* 3.9 24.4 + - + +
56A GLY* 4.1 18.8 + - - -
30B LYS 2.7 17.1 + - - +
31B ALA* 3.2 9.8 + - - +
33B ILE* 1.3 75.0 - - - +
35B GLU* 1.3 63.5 + - - +
38B GLY* 2.8 36.1 + - - +
39B ILE 3.3 30.1 - - - +
40B PRO* 4.3 2.2 - - + -
41B PRO* 4.0 10.5 - - + -
44B GLN* 3.6 0.6 - - - +
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Residues in contact with GLU 35 (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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23A ASN 5.5 0.9 - - - +
24A ASP* 2.9 28.2 - - - +
25A SER* 2.9 26.1 + - - +
28A ALA* 3.5 17.2 - - - +
31B ALA 3.0 16.3 + - - +
32B LYS* 3.4 15.4 + - - +
33B ILE 3.2 0.2 - - - -
34B GLN* 1.3 92.8 + - - +
36B LYS* 1.3 61.3 + - + +
38B GLY* 4.7 0.9 + - - -
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Residues in contact with LYS 36 (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 ILE* 3.9 35.2 - - + +
17B THR* 3.9 21.4 + - - +
18B LEU* 4.7 9.8 - - + +
32B LYS 3.2 16.7 + - - +
33B ILE* 4.5 1.6 - - - +
35B GLU* 1.3 79.7 - - + +
37B GLU* 1.3 79.6 + - + +
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Residues in contact with GLU 37 (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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10B THR* 4.3 19.6 - - - +
16B ILE* 3.8 22.2 - - + +
33B ILE* 2.9 27.4 + - + +
36B LYS* 1.3 100.3 - - + +
38B GLY* 1.3 61.4 + - - +
39B ILE* 3.3 26.5 + - + +
72B LEU* 4.8 5.2 - - + -
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Residues in contact with GLY 38 (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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34B GLN* 2.8 28.6 + - - -
35B GLU 4.5 1.3 + - - -
36B LYS 3.6 0.8 - - - -
37B GLU* 1.3 79.5 - - - +
39B ILE* 1.3 61.1 + - - +
40B PRO* 3.7 6.9 - - - +
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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
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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