Contacts of the strand formed by residues 94 - 110 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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90B MET* 3.6 3.3 - - - -
91B GLU* 3.4 35.7 + - + +
92B GLY 3.3 3.2 - - - -
93B ASN* 1.3 96.4 + - - +
95B ALA* 1.3 76.8 + - - +
96B SER* 3.8 6.9 + - - -
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Residues in contact with ALA 95 (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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37B MET* 4.2 24.0 - - + -
88B LEU* 4.6 13.7 - - + -
89B THR 3.2 10.5 - - - +
90B MET* 4.2 2.2 - - - +
93B ASN 3.7 5.0 + - - +
94B GLN* 1.3 86.7 + - - +
96B SER* 1.3 63.5 + - - +
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Residues in contact with SER 96 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88B LEU* 3.9 6.9 - - - +
89B THR* 2.7 57.4 + - - -
91B GLU* 6.1 0.9 - - - +
94B GLN* 4.6 7.0 + - - -
95B ALA* 1.3 76.2 - - - +
97B TRP* 1.3 64.7 + - - +
98B ARG* 3.4 25.6 + - - -
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Residues in contact with TRP 97 (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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42A LEU* 3.9 25.2 - - + +
43A ASP* 3.6 23.0 + - - -
47A TYR* 5.8 2.9 - + - -
200A L44 3.3 85.7 - - + +
40B VAL* 3.7 29.2 - - + -
42B LEU* 5.3 1.6 - - + -
49B GLU* 4.1 4.5 - - - -
86B LYS* 4.1 22.0 - - + -
87B ALA 3.4 23.6 - - - -
88B LEU* 3.4 33.2 - - + +
96B SER* 1.3 75.7 - - - +
98B ARG* 1.3 66.3 + - - +
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Residues in contact with ARG 98 (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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200A L44 5.8 0.2 - - - -
28B ASP* 4.5 23.1 + - + +
29B ILE* 6.2 1.1 - - + -
32B ASN* 5.4 8.3 - - - +
34B VAL* 3.5 27.1 - - - +
86B LYS* 4.2 7.3 - - - +
87B ALA 3.0 30.0 + - - +
89B THR* 3.9 22.0 + - + +
91B GLU* 3.8 28.9 + - - +
96B SER* 3.4 18.1 + - - +
97B TRP* 1.3 80.6 - - - +
99B PHE* 1.3 68.1 + - - +
100B ILE* 3.2 6.6 + - + +
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Residues in contact with PHE 99 (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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20A TRP* 4.0 32.1 - + - -
50A TYR* 5.3 7.0 - + + -
200A L44 4.0 15.7 - - + -
28B ASP* 3.5 3.3 - - - +
29B ILE* 2.8 58.1 + - + +
84B PHE* 4.0 17.9 - - + -
85B ILE 3.4 5.2 - - - -
86B LYS* 3.7 56.5 - - + -
98B ARG* 1.3 71.5 - - - +
100B ILE* 1.3 59.0 + - - +
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Residues in contact with ILE 100 (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 LYS* 5.3 0.7 - - + -
26B ALA* 4.2 24.0 - - + -
27B THR 3.5 12.1 - - - +
28B ASP* 4.9 1.6 - - - -
34B VAL* 4.7 7.4 - - + -
36B VAL* 4.4 6.3 - - + -
51B PHE* 4.0 21.3 - - + -
84B PHE* 3.3 7.0 - - - -
85B ILE* 2.8 35.5 + - + +
87B ALA* 3.5 27.8 - - + -
89B THR* 4.3 15.3 - - + -
98B ARG* 3.6 14.4 - - + +
99B PHE* 1.3 75.2 - - - +
101B ARG* 1.3 70.9 + - - +
102B ILE* 4.4 11.9 - - + -
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Residues in contact with ARG 101 (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 LYS* 5.0 2.9 + - - -
26B ALA* 5.2 1.9 - - - +
27B THR* 2.9 38.3 + - - +
28B ASP 3.7 15.2 + - - +
29B ILE 3.8 16.8 + - - -
31B GLY* 5.2 3.8 - - - +
82B ASP* 3.2 33.9 + - - +
83B THR 3.3 6.3 - - - +
84B PHE* 3.6 43.4 - - + -
100B ILE* 1.3 76.3 - - - +
102B ILE* 1.3 73.3 + - - +
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Residues in contact with ILE 102 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23B LYS* 4.0 30.1 - - + +
51B PHE* 4.2 23.6 - - + -
52B PHE 3.6 17.7 - - - +
53B GLU* 3.5 25.8 - - + +
82B ASP* 3.2 4.2 - - - -
83B THR* 2.7 48.4 + - + +
85B ILE* 4.1 18.2 - - + -
100B ILE* 4.4 14.4 - - + -
101B ARG* 1.3 84.0 - - - +
103B GLU* 1.3 66.3 + - - +
104B THR* 3.3 1.6 + - + -
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Residues in contact with GLU 103 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53B GLU* 3.2 14.9 + - + +
54B THR 2.5 46.7 + - - +
55B LYS* 2.6 40.2 + - + +
80B GLU* 3.5 36.8 - - + +
81B THR 3.2 5.8 - - - -
82B ASP* 3.4 15.9 - - - +
102B ILE* 1.3 74.0 - - - +
104B THR* 1.3 52.1 + - - +
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Residues in contact with THR 104 (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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81A THR* 4.5 1.9 + - - -
82A ASP 4.7 3.8 - - - +
83A THR* 3.5 29.4 - - - +
104A THR* 3.2 36.3 + - - +
52B PHE* 4.3 10.1 - - + +
54B THR* 3.2 24.1 + - - +
81B THR* 2.8 10.8 + - - -
82B ASP 3.6 2.4 + - - -
83B THR* 3.4 33.7 + - + -
102B ILE 4.1 0.4 - - - +
103B GLU* 1.3 74.8 - - - +
105B ALA* 1.3 64.6 + - - +
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Residues in contact with ALA 105 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81A THR* 3.8 11.9 - - + +
105A ALA* 3.6 29.8 - - + -
107A VAL* 4.6 8.1 - - + -
54B THR* 3.8 15.0 + - + -
56B CYS* 5.2 0.2 - - - -
79B THR 3.7 0.5 - - - +
80B GLU* 3.1 6.0 - - - +
81B THR* 2.9 31.8 + - - +
103B GLU 3.8 1.2 - - - -
104B THR* 1.3 84.2 + - - +
106B CYS* 1.3 61.7 + - - +
107B VAL* 4.0 1.1 + - + -
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Residues in contact with CYS 106 (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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107A VAL* 4.2 10.9 - - - +
13B VAL* 5.9 1.4 - - - +
14B CYS* 4.2 13.0 + - + +
15B ASP 3.4 20.4 - - - +
16B SER* 4.1 13.6 - - - -
54B THR* 4.9 0.2 - - - +
56B CYS* 2.0 59.9 - - + +
78B CYS* 3.6 22.0 - - - -
79B THR 3.6 2.5 - - - -
105B ALA* 1.3 73.2 - - - +
107B VAL* 1.3 62.4 + - - +
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Residues in contact with VAL 107 (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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12A SER* 4.5 12.6 - - - +
13A VAL* 6.1 0.7 - - + -
105A ALA* 4.8 4.5 - - + -
106A CYS 4.4 8.5 - - - +
107A VAL* 4.1 22.4 - - + +
13B VAL* 6.1 0.7 - - - -
78B CYS* 3.1 8.0 - - - -
79B THR* 2.9 40.0 + - - +
81B THR* 3.8 32.8 - - + +
105B ALA* 4.7 2.2 - - + -
106B CYS* 1.3 77.8 - - - +
108B CYS* 1.3 64.6 + - - +
109B VAL* 3.7 13.9 + - + +
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Residues in contact with CYS 108 (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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12A SER* 3.6 9.4 + - - -
13A VAL* 3.4 43.0 + - + +
13B VAL* 4.2 12.0 - - + +
66B CYS* 2.0 51.4 - - + -
69B ILE* 3.6 22.0 - - - -
76B SER* 3.9 3.8 - - - -
78B CYS* 3.4 10.6 - - - -
107B VAL* 1.3 74.9 - - - +
109B VAL* 1.3 62.9 + - - +
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Residues in contact with VAL 109 (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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10A GLU* 3.7 37.9 - - + +
11A HIS 3.3 16.6 - - - +
12A SER* 4.8 1.6 - - - +
75B ASN 3.7 0.2 - - - +
76B SER* 3.1 8.0 - - - -
77B TYR* 2.8 61.3 + - + +
79B THR* 4.6 7.9 - - - +
107B VAL* 4.0 16.6 - - + +
108B CYS* 1.3 79.1 - - - +
110B ILE* 1.3 62.0 + - - +
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Residues in contact with ILE 110 (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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10A GLU* 3.5 1.4 - - - -
11A HIS* 2.6 59.8 + - + +
12A SER 4.1 1.8 - - - +
13A VAL* 3.9 11.2 - - + -
67A ARG* 3.8 50.5 - - + +
68A GLY* 4.1 2.0 - - - +
69B ILE* 3.5 31.6 - - + -
74B TRP* 3.8 26.7 - - + -
75B ASN 3.2 11.0 - - - +
76B SER* 3.9 1.8 - - - -
108B CYS* 4.4 0.2 - - - -
109B VAL* 1.3 79.7 - - - +
111B THR* 1.3 61.8 + - - +
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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