Contacts of the strand formed by residues 42 - 56 (chain B) in PDB entry 3GAX
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 TYR 42 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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19A GLU* 5.7 1.3 + - - -
35B ASN* 4.2 0.9 - - - +
40B ASP* 2.8 29.3 + - - +
41B MET* 1.3 107.4 - - + +
43B HIS* 1.3 63.9 + - - +
44B SER* 3.7 1.7 + - - -
70B ARG* 3.4 25.4 - - + +
71B THR 3.9 12.3 - - - +
72B THR* 3.6 19.5 - - - -
73B CYS 3.4 14.8 - - - +
74B THR* 3.2 27.1 - - + +
75B LYS* 3.6 11.8 - - - -
86B HIS* 5.8 2.7 - - - -
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Residues in contact with HIS 43 (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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31B VAL* 5.2 2.5 - - + -
35B ASN* 3.3 32.9 + - + +
42B TYR* 1.3 72.8 - - - +
44B SER* 1.3 67.8 + - - +
45B ARG* 4.0 24.6 - - + +
70B ARG* 4.0 0.5 - - - -
71B THR* 2.8 42.2 + - + +
73B CYS* 2.8 23.9 + - + +
74B THR 4.8 4.5 - - - +
75B LYS* 4.3 11.3 - - + +
79B ASN* 3.9 27.0 + - - +
83B CYS* 4.5 6.1 - - - -
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Residues in contact with SER 44 (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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31B VAL* 3.5 5.8 - - - +
34B TYR* 3.9 25.6 + - - -
35B ASN* 2.8 35.6 + - - -
40B ASP* 4.4 5.9 + - - +
42B TYR 3.7 0.9 + - - -
43B HIS* 1.3 77.2 + - - +
45B ARG* 1.3 65.1 + - - +
68B LEU* 4.7 9.2 - - - -
69B CYS 3.3 11.4 - - - -
70B ARG* 3.7 24.8 + - - +
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Residues in contact with ARG 45 (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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45A ARG* 3.1 38.4 - - - +
46A ALA 4.7 2.6 + - - -
81A ASP 4.1 5.5 + - - -
82A ASN* 5.5 1.8 - - - +
31B VAL* 4.1 6.7 - - + -
43B HIS* 4.0 18.2 - - - +
44B SER* 1.3 75.7 - - - +
46B ALA* 1.3 64.3 + - - +
47B CYS 3.3 0.5 + - - -
68B LEU* 3.4 9.2 - - - -
69B CYS 2.9 30.0 + - - +
71B THR* 3.1 14.3 - - + +
82B ASN 4.0 15.9 + - - +
83B CYS* 2.6 34.3 + - - -
84B PRO* 4.0 3.6 - - - +
85B PHE* 3.3 39.6 - - + -
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Residues in contact with ALA 46 (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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45A ARG* 4.8 3.1 + - - -
85A PHE* 3.6 18.4 - - - -
27B LEU* 4.5 18.8 - - + -
31B VAL* 4.8 3.5 - - + +
45B ARG* 1.3 74.0 + - - +
47B CYS* 1.3 61.3 + - - +
48B GLN 3.3 10.5 - - - +
49B VAL* 4.5 9.5 - - + +
66B VAL* 4.3 9.6 - - + -
67B GLU 3.3 11.9 - - - +
68B LEU* 3.4 13.3 - - + +
85B PHE* 3.7 4.5 - - - -
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Residues in contact with CYS 47 (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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47A CYS* 3.9 25.1 - - - +
69A CYS* 5.6 0.2 - - - -
85A PHE* 3.6 14.8 - - - +
45B ARG 3.3 1.8 + - - -
46B ALA* 1.3 72.6 - - - +
48B GLN* 1.3 60.2 + - - +
67B GLU* 2.9 31.7 + - - +
68B LEU 3.5 1.8 - - - -
69B CYS* 2.1 50.9 - - + -
85B PHE* 3.6 24.5 - - + -
94B LYS* 4.6 3.1 - - - -
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Residues in contact with GLN 48 (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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85A PHE* 5.0 4.3 - - - -
86A HIS 6.0 0.2 - - - +
92A LYS* 3.6 26.5 + - + +
94A LYS* 6.0 1.8 - - - +
46B ALA* 3.3 1.6 - - - +
47B CYS* 1.3 82.5 - - - +
49B VAL* 1.3 71.0 + - - +
50B VAL* 3.9 19.8 - - + +
66B VAL* 3.3 7.8 - - - +
67B GLU* 2.9 69.0 + - + +
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Residues in contact with VAL 49 (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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84A PRO* 5.0 0.7 - - + -
85A PHE* 3.7 32.4 + - + +
86A HIS 4.3 2.4 + - - +
87A ASP* 3.4 29.9 - - + +
92A LYS* 5.6 1.2 + - - -
18B VAL* 3.6 19.7 - - + -
23B VAL* 5.8 0.4 - - + -
27B LEU* 3.9 26.2 - - + -
46B ALA* 4.5 10.8 - - + +
48B GLN* 1.3 80.5 - - - +
50B VAL* 1.3 63.5 + - - +
51B ARG 4.5 10.5 - - - +
52B ALA* 5.0 4.5 - - + -
64B LEU* 5.9 3.8 - - + -
65B ASP 4.0 8.5 - - - +
66B VAL* 4.3 7.9 - - + -
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Residues in contact with VAL 50 (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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87A ASP* 4.6 9.3 - - - +
48B GLN* 3.9 25.1 - - + +
49B VAL* 1.3 75.9 - - - +
51B ARG* 1.3 63.1 + - + +
65B ASP* 2.8 26.4 + - + +
66B VAL* 4.3 6.3 - - - -
67B GLU* 4.0 25.6 - - + +
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Residues in contact with ARG 51 (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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87A ASP* 5.2 3.6 - - - -
15B ASP* 5.9 1.3 - - - +
49B VAL* 3.6 5.0 - - - +
50B VAL* 1.3 83.5 - - + +
52B ALA* 1.3 65.2 - - - +
53B ARG* 3.8 51.8 - - + +
63B PHE 3.9 0.6 - - - +
64B LEU* 3.5 2.9 - - - +
65B ASP* 2.5 73.0 + - + +
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Residues in contact with ALA 52 (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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87A ASP* 4.5 7.9 + - - +
15B ASP* 4.0 2.3 - - - +
16B ALA* 3.0 43.4 + - + +
17B SER* 4.2 4.9 - - - +
18B VAL 4.7 0.9 - - - +
23B VAL* 4.0 16.8 - - + -
49B VAL* 5.0 5.4 - - + -
51B ARG* 1.3 76.6 - - - +
53B ARG* 1.3 65.8 + - - +
63B PHE 3.5 5.2 - - - -
64B LEU* 3.8 16.4 - - + -
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Residues in contact with ARG 53 (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 PRO* 4.4 24.4 - - + +
14B MET 3.1 16.6 - - - +
15B ASP* 4.0 15.3 - - - +
16B ALA* 4.0 4.4 - - - +
51B ARG* 3.8 52.8 - - + +
52B ALA* 1.3 78.5 - - - +
54B LYS* 1.3 64.5 + - - +
62B TYR* 3.5 5.9 - - - +
63B PHE* 2.9 62.6 + - + +
64B LEU* 4.5 0.9 - - - +
65B ASP* 4.4 5.3 + - - -
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Residues in contact with LYS 54 (chain B).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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13B PRO* 3.4 2.0 - - - +
14B MET* 2.8 58.7 + - + +
15B ASP 5.2 0.4 - - - +
16B ALA* 4.3 8.7 - - + +
20B GLU* 2.6 34.1 + - - +
53B ARG* 1.3 77.4 - - - +
55B GLN* 1.3 62.9 + - - +
56B ILE* 4.2 18.8 - - + -
60B VAL* 4.0 7.6 - - + -
61B ASN 3.1 12.8 - - - +
62B TYR* 3.9 27.8 + - + -
63B PHE* 4.3 2.2 - - - -
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Residues in contact with GLN 55 (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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12B GLY* 3.8 33.7 - - - +
13B PRO* 4.0 13.0 - - + +
14B MET* 5.5 2.0 - - - -
54B LYS* 1.3 76.5 - - - +
56B ILE* 1.3 69.3 + - - +
57B VAL* 3.5 16.5 + - + +
60B VAL* 3.4 2.4 - - - -
61B ASN* 2.8 50.2 + - + +
63B PHE* 3.8 23.6 - - + -
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Residues in contact with ILE 56 (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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12B GLY 5.5 0.2 + - - -
14B MET* 5.1 14.8 - - + +
54B LYS* 4.2 20.6 - - + -
55B GLN* 1.3 77.7 - - - +
57B VAL* 1.3 75.3 + - - +
59B GLY 3.5 7.9 - - - +
60B VAL* 3.9 26.9 - - + -
106B TRP* 5.8 4.3 - - + -
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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