Contacts of the strand formed by residues 94 - 112 (chain A) in PDB entry 4EC7
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 GLN 94 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90A MET* 3.3 2.4 - - - -
91A GLU* 3.0 35.3 + - + +
92A GLY 3.6 0.2 - - - -
93A ASN* 1.3 89.5 - - - +
95A ALA* 1.3 63.7 + - - +
96A SER* 3.8 5.7 + - - -
98A ARG* 5.0 2.0 + - - +
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Residues in contact with ALA 95 (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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37A MET* 5.6 2.7 - - - -
88A LEU* 4.9 10.5 - - + -
89A THR 3.3 13.7 - - - +
90A MET* 3.7 10.3 - - + +
93A ASN 3.6 5.5 + - - +
94A GLN* 1.3 71.0 - - - +
96A SER* 1.3 64.3 + - - +
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Residues in contact with SER 96 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88A LEU* 3.5 9.0 - - - +
89A THR* 2.8 37.7 + - - -
94A GLN* 4.1 4.6 + - - -
95A ALA* 1.3 77.3 - - - +
97A TRP* 1.3 63.2 + - - +
98A ARG* 2.9 38.6 + - - -
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Residues in contact with TRP 97 (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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40A VAL* 3.3 33.7 - - + -
41A ASN 6.1 0.2 - - - -
42A LEU* 4.8 4.9 - - + -
49A GLU* 4.3 0.9 - - - -
86A LYS* 3.7 14.1 - - + -
87A ALA 3.5 20.6 - - - -
88A LEU* 3.5 30.7 - - + +
96A SER* 1.3 75.3 - - - +
98A ARG* 1.3 62.3 + - - +
200A L44 3.4 109.2 - - + +
42B LEU* 4.4 13.5 - - + +
47B TYR* 5.8 3.1 - - - -
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Residues in contact with ARG 98 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28A ASP* 2.8 33.4 + - + -
30A LYS* 3.9 20.1 - - - +
32A ASN* 3.2 10.9 - - - +
34A VAL* 4.5 5.9 - - - +
85A ILE 3.6 0.2 - - - +
86A LYS* 3.3 4.6 - - - +
87A ALA* 2.6 40.7 + - - +
89A THR* 3.1 30.2 + - + +
91A GLU* 2.8 47.4 + - - +
94A GLN* 5.0 2.6 + - - +
96A SER* 2.9 23.1 + - - +
97A TRP* 1.3 77.7 - - - +
99A PHE* 1.3 66.1 + - - +
100A ILE* 3.7 2.3 + - - +
200A L44 5.3 2.9 - - - -
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Residues in contact with PHE 99 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28A ASP* 3.3 6.6 - - - +
29A ILE* 2.9 38.3 + - + +
30A LYS* 4.6 3.4 - - - +
84A PHE* 3.9 11.7 - - + -
85A ILE 3.3 2.9 - - - +
86A LYS* 3.4 40.6 - - + -
98A ARG* 1.3 72.6 - - - +
100A ILE* 1.3 60.4 + - - +
200A L44 3.3 56.3 - - + -
20B TRP* 3.5 42.6 - + + -
50B TYR* 4.0 23.8 - + + -
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Residues in contact with ILE 100 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23A LYS* 5.2 3.4 - - + -
26A ALA* 3.8 12.3 - - + -
27A THR 3.7 7.2 - - - +
28A ASP* 4.5 4.3 - - + -
34A VAL* 4.4 14.1 - - + -
36A VAL* 3.7 24.0 - - + -
51A PHE* 3.8 26.2 - - + -
84A PHE* 3.3 6.9 - - - -
85A ILE 2.6 42.0 + - - +
87A ALA* 4.0 4.5 - - + -
89A THR* 3.9 26.7 - - + -
98A ARG 4.1 4.9 - - - +
99A PHE* 1.3 77.7 - - - +
101A ARG* 1.3 61.3 + - - +
102A ILE* 3.4 17.7 + - + +
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Residues in contact with ARG 101 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23A LYS* 5.3 6.1 - - - +
26A ALA* 5.0 8.1 - - - +
27A THR* 2.8 56.6 + - - +
28A ASP 3.3 12.3 + - - -
29A ILE 4.2 10.1 + - - -
31A GLY* 4.9 3.2 - - - +
82A ASP* 3.1 38.0 + - + +
83A THR 3.6 6.3 - - - -
84A PHE* 3.5 32.7 - - + -
100A ILE* 1.3 69.9 - - - +
102A ILE* 1.3 61.2 + - - +
103A GLU* 4.3 1.1 + - + +
200A L44 6.1 0.8 - - - +
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Residues in contact with ILE 102 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21A VAL* 6.1 0.4 - - + -
23A LYS* 4.8 12.1 - - + +
51A PHE* 3.7 33.0 - - + -
52A PHE 3.8 20.0 - - - +
53A GLU* 4.0 14.8 - - + +
82A ASP* 3.5 2.9 - - - -
83A THR* 2.7 53.6 + - + +
85A ILE* 3.8 11.4 - - + -
100A ILE* 3.4 38.8 - - + +
101A ARG* 1.3 74.6 - - - +
103A GLU* 1.3 72.5 + - - +
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Residues in contact with GLU 103 (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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53A GLU* 3.5 16.2 + - + +
54A THR 2.8 35.8 + - - +
55A LYS* 3.3 32.5 + - - +
80A GLU* 3.0 36.0 - - + +
81A THR 3.7 0.7 - - - -
82A ASP* 3.3 20.6 - - - +
101A ARG* 4.3 1.5 + - + +
102A ILE* 1.3 80.1 - - - +
104A THR* 1.3 56.8 + - - +
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Residues in contact with THR 104 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52A PHE* 5.0 2.3 + - - -
54A THR* 3.2 24.1 + - - +
81A THR* 2.9 20.9 + - - +
82A ASP 3.7 5.6 - - - +
83A THR* 3.4 29.1 - - - +
102A ILE* 3.4 0.6 + - - -
103A GLU* 1.3 72.5 - - - +
105A ALA* 1.3 65.6 + - + +
81B THR* 4.8 2.3 + - - -
82B ASP 5.2 3.5 + - - +
83B THR* 3.7 14.6 + - - -
104B THR* 3.2 47.5 + - - +
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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
----------------------------------------------------------
54A THR* 3.4 14.7 + - - -
80A GLU* 3.0 8.8 - - - +
81A THR* 3.0 29.6 + - - +
104A THR* 1.3 84.8 - - + +
106A CYS* 1.3 61.1 + - - +
107A VAL* 4.0 6.1 - - + -
81B THR* 4.2 9.4 - - - +
105B ALA* 3.6 31.4 - - + -
107B VAL* 4.8 4.3 - - + -
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Residues in contact with CYS 106 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12A SER* 4.9 3.3 + - - -
13A VAL* 5.9 0.9 - - - +
14A CYS* 4.1 8.1 - - + +
15A ASP 3.5 12.3 - - - +
16A SER* 3.7 28.3 - - - -
56A CYS* 2.0 61.2 - - - +
58A ASN 4.7 0.4 - - - -
78A CYS* 3.6 20.9 - - - -
79A THR 3.8 0.2 - - - -
105A ALA* 1.3 74.5 - - - +
107A VAL* 1.3 62.8 + - - +
107B VAL* 4.4 9.9 - - - +
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Residues in contact with VAL 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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13A VAL* 5.9 0.9 - - - -
78A CYS* 3.3 5.1 - - - -
79A THR* 2.8 41.5 + - + +
81A THR* 3.5 33.2 - - + +
105A ALA* 4.3 10.3 - - + -
106A CYS* 1.3 77.0 - - - +
108A CYS* 1.3 63.1 + - - +
109A VAL* 3.8 15.8 + - + +
12B SER* 5.7 3.8 - - - +
13B VAL* 5.8 2.7 - - + -
105B ALA* 4.6 3.8 - - + -
106B CYS 4.2 11.0 - - - +
107B VAL* 4.1 22.2 - - + -
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Residues in contact with CYS 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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13A VAL* 3.7 22.1 - - + +
14A CYS* 4.1 1.8 - - - +
66A CYS* 2.0 53.4 - - + -
69A ILE* 4.2 3.1 - - - -
76A SER* 3.8 11.0 - - - -
77A TYR 3.5 1.3 - - - -
78A CYS* 3.5 4.0 - - - -
107A VAL* 1.3 76.2 - - - +
109A VAL* 1.3 66.0 + - - +
110A ILE* 4.0 1.3 - - - -
12B SER* 4.5 1.4 + - - -
13B VAL* 3.3 45.7 + - + +
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Residues in contact with VAL 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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76A SER* 3.3 4.5 - - - -
77A TYR* 2.9 75.7 + - + +
79A THR* 4.2 12.1 - - + -
107A VAL* 4.1 16.6 - - + +
108A CYS* 1.3 79.3 - - - +
110A ILE* 1.3 64.1 + - - +
111A THR 4.3 0.2 + - - -
10B GLU* 4.5 8.7 - - + +
11B HIS 3.5 11.4 - - - +
12B SER* 4.9 7.4 - - - +
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Residues in contact with ILE 110 (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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69A ILE* 4.1 9.9 - - + -
74A TRP* 3.9 29.8 - - + -
75A ASN 3.4 4.5 - - - +
76A SER* 4.0 9.2 - - - -
108A CYS* 4.0 7.6 - - - -
109A VAL* 1.3 78.8 - - - +
111A THR* 1.3 63.0 + - - +
10B GLU* 3.3 3.0 - - - +
11B HIS* 2.7 59.3 + - + +
12B SER 3.9 6.5 - - - +
13B VAL* 3.4 23.6 - - + -
67B ARG* 3.7 42.0 - - + +
68B GLY* 4.1 1.8 - - - +
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Residues in contact with THR 111 (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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74A TRP* 3.9 2.7 - - - -
75A ASN* 2.8 38.8 + - + +
77A TYR* 5.0 2.8 - - - -
109A VAL 4.3 0.4 + - - -
110A ILE* 1.3 73.3 - - - +
112A LYS* 1.3 76.0 + - - +
113A LYS* 3.0 6.2 + - - -
116A ASN* 6.2 0.2 - - - +
9B GLY* 3.2 21.3 - - - +
10B GLU* 3.0 32.9 + - + +
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Residues in contact with LYS 112 (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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73A HIS* 4.1 26.6 - - - +
74A TRP* 3.3 52.3 - - + +
110A ILE 4.2 0.4 + - - -
111A THR* 1.3 78.1 - - - +
113A LYS* 1.3 69.2 + - - +
114A LYS* 3.7 9.7 + - + +
9B GLY 4.2 4.1 + - - +
11B HIS* 4.8 11.7 + - + -
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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
------------------------------------------------------------
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