Contacts of the strand formed by residues 93 - 109 (chain A) in PDB entry 4FAO
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 PRO 93 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27A ILE* 4.0 16.6 - - + -
85A LEU* 4.2 12.3 - - + -
86A TYR 3.6 7.2 - - - +
87A LYS* 4.8 1.3 - - + -
91A GLY 3.6 3.4 - - - +
92A VAL* 1.3 88.7 - - + +
94A THR* 1.3 62.7 + - - +
46E ARG* 3.4 26.0 - - - +
55E VAL* 3.8 26.0 - - + +
56E LYS* 3.4 16.8 + - - +
81E VAL* 3.6 31.0 - - + -
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Residues in contact with THR 94 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85A LEU* 3.1 7.5 - - - +
86A TYR* 2.9 61.5 + - - -
88A ASP* 3.8 19.4 - - - +
92A VAL* 2.8 19.8 + - + +
93A PRO* 1.3 74.4 - - - +
95A LEU* 1.3 61.8 + - - +
21E GLU* 3.1 30.3 - - + +
56E LYS* 3.8 6.7 - - - +
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Residues in contact with LEU 95 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83A SER* 4.4 0.4 - - - -
84A VAL 3.2 23.8 - - - +
85A LEU* 4.3 7.0 - - + +
86A TYR* 4.4 2.7 - - - -
94A THR* 1.3 78.8 - - - +
96A LYS* 1.3 76.6 + - - +
97A TYR* 3.5 18.1 + - + +
13E TYR* 6.4 1.8 - - + -
21E GLU* 5.6 0.2 + - - -
42E TYR* 3.0 41.7 - - + +
56E LYS* 4.0 10.5 - - - +
59E CYS 4.2 8.5 - - - +
60E TRP* 3.9 19.7 - - + -
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Residues in contact with LYS 96 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82A ILE 4.0 1.7 - - - +
83A SER* 3.4 0.5 - - - -
84A VAL* 2.9 40.6 + - + +
86A TYR* 3.9 16.8 - - + +
95A LEU* 1.3 78.9 + - - +
97A TYR* 1.3 80.4 + - - +
98A HIS* 3.3 45.7 - - - +
99A TYR* 4.0 19.1 + - + +
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Residues in contact with TYR 97 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82A ILE 3.4 8.7 - - - +
83A SER* 2.8 40.4 + - - -
95A LEU* 3.5 17.4 + - + +
96A LYS* 1.3 86.2 - - - +
98A HIS* 1.3 87.3 + + + +
29E GLU* 5.6 7.0 - - - +
31E CYS* 4.0 5.5 - - - +
32E GLU* 2.8 38.4 + - + -
39E LEU* 4.0 2.4 - - - +
59E CYS* 3.4 48.3 - - + +
60E TRP* 3.5 6.4 + - - -
61E LEU* 3.6 25.1 - - + +
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Residues in contact with HIS 98 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81A PRO* 4.1 18.2 - - + +
96A LYS* 3.3 22.3 - - - +
97A TYR* 1.3 109.0 - + + +
99A TYR* 1.3 59.2 + - - +
100A GLU* 3.2 35.1 + - + +
32E GLU* 4.3 17.9 + - + +
33E GLY* 5.6 1.2 - - - -
61E LEU* 4.3 8.8 - - + +
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Residues in contact with TYR 99 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17A PHE* 6.3 1.3 - + - -
22A TRP* 4.5 8.6 - + - -
25A TRP* 4.0 17.9 - + - -
26A ILE* 5.4 1.8 - - + -
81A PRO* 3.1 17.4 - - - +
82A ILE* 3.1 23.8 + - + +
84A VAL* 3.9 32.5 - - + -
96A LYS* 4.0 21.9 - - + +
97A TYR 3.6 0.2 - - - -
98A HIS* 1.3 70.6 - - - +
100A GLU* 1.3 69.2 + - - +
102A MET* 3.7 29.8 - - + +
53B LYS* 3.5 28.5 - - + +
75C GLU* 2.6 30.6 + - - +
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Residues in contact with GLU 100 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79A LEU 4.3 5.4 - - - +
81A PRO* 3.5 22.4 - - - +
98A HIS* 3.2 36.7 + - + +
99A TYR* 1.3 78.8 - - - +
101A GLY* 1.3 68.0 + - - +
102A MET* 3.7 0.5 + - - +
53B LYS* 3.7 22.0 - - - +
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Residues in contact with GLY 101 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79A LEU* 3.8 29.8 + - - +
80A SER 3.7 9.3 + - - -
99A TYR 3.7 1.2 + - - -
100A GLU* 1.3 80.8 + - - +
102A MET* 1.3 59.9 + - - +
103A SER 3.7 1.1 - - - -
52B THR* 5.8 0.2 - - - -
53B LYS* 2.9 10.4 + - - +
54B HIS* 2.8 26.5 + - - +
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Residues in contact with MET 102 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17A PHE* 4.3 12.1 - - + -
22A TRP* 4.7 4.5 - - + -
32A TYR* 2.9 59.0 + - + +
34A ALA* 3.4 7.3 - - - +
80A SER 3.2 3.4 + - - -
82A ILE* 3.8 29.6 - - + -
99A TYR* 3.7 39.5 - - + +
100A GLU 3.9 4.0 - - - +
101A GLY* 1.3 79.3 - - - +
103A SER* 1.3 60.2 + - - +
53B LYS* 3.6 24.5 - - + -
54B HIS* 3.8 11.6 - - - +
57B VAL* 4.2 15.3 - - + -
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Residues in contact with SER 103 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32A TYR* 4.7 0.2 - - - -
33A GLU 3.1 23.6 + - - -
34A ALA* 4.2 4.3 - - - +
35A TYR* 3.6 13.5 - - - -
79A LEU* 3.0 11.8 - - - +
80A SER* 3.0 41.9 + - - -
82A ILE* 4.2 15.5 - - - -
101A GLY 3.7 0.6 - - - -
102A MET* 1.3 80.9 - - - +
104A VAL* 1.3 63.4 + - - +
54B HIS* 4.3 0.4 - - - -
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Residues in contact with VAL 104 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10A LYS* 3.8 16.1 + - + -
35A TYR* 3.2 44.7 - - + +
36A GLU* 4.4 1.1 - - - +
37A CYS* 3.9 19.3 - - - -
76A PRO* 4.1 18.2 - - + -
79A LEU* 3.8 3.6 - - + -
80A SER* 4.8 1.6 - - - -
103A SER* 1.3 75.6 + - - +
105A ALA* 1.3 63.3 + - - +
106A GLU 3.7 21.1 - - - +
54B HIS* 3.3 34.5 - - + +
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Residues in contact with ALA 105 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10A LYS* 3.2 25.2 + - - +
78A LYS* 2.8 47.3 + - + +
79A LEU 4.0 1.6 - - - +
80A SER* 4.1 19.7 - - - +
103A SER 3.6 1.6 + - - -
104A VAL* 1.3 73.4 - - - +
106A GLU* 1.3 64.5 - - + +
34E GLU* 4.8 1.3 - - - +
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Residues in contact with GLU 106 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10A LYS* 5.1 1.6 - - - +
50A THR* 5.7 1.4 + - - -
76A PRO* 3.6 4.9 - - - +
77A THR* 2.8 35.1 + - - +
78A LYS* 3.4 39.3 + - + +
104A VAL* 3.7 5.9 - - - +
105A ALA* 1.3 84.6 - - + +
107A CYS* 1.3 62.2 + - - +
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Residues in contact with CYS 107 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8A CYS* 4.8 1.8 - - - -
9A GLN* 3.7 22.2 - - - -
10A LYS* 3.7 22.9 - - + +
37A CYS* 2.0 52.3 - - + -
48A ASP 4.4 9.7 - - - +
49A VAL* 5.3 0.9 - - - -
50A THR* 4.2 8.5 + - - -
74A CYS* 4.6 5.8 - - - -
75A VAL 3.5 4.3 - - - -
77A THR* 3.3 11.4 + - - +
104A VAL* 4.2 0.7 - - - -
106A GLU* 1.3 75.7 - - - +
108A GLY* 1.3 57.7 + - - +
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Residues in contact with GLY 108 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8A CYS* 4.5 5.1 - - - -
49A VAL* 3.4 20.4 - - - -
73A CYS 3.4 0.3 - - - +
74A CYS* 3.3 6.2 - - - -
75A VAL* 2.9 34.5 + - - +
77A THR* 3.5 13.7 - - - -
107A CYS* 1.3 79.2 - - - +
109A CYS* 1.3 61.6 + - - -
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Residues in contact with CYS 109 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8A CYS* 4.2 9.0 - - - -
41A CYS* 2.0 55.6 - - + -
45A LEU* 4.7 13.9 - - + -
49A VAL* 3.1 33.6 + - + +
51A PRO* 3.9 4.9 - - + +
52A THR 4.0 0.2 + - - -
55A ALA* 3.8 11.8 - - + +
72A ALA* 4.3 5.2 - - + -
73A CYS 3.4 2.5 - - - -
108A GLY* 1.3 73.6 - - - -
110A ARG* 1.3 83.0 + - - +
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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
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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