Contacts of the strand formed by residues 92 - 104 (chain A) in PDB entry 3CJE
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 ASP 92 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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19A ASN* 2.5 41.6 + - - +
20A GLY 3.2 5.6 - - - -
21A LYS* 3.5 14.3 - - + +
90A ASP 3.3 5.3 + - - +
91A LEU* 1.3 74.5 - - - +
93A VAL* 1.3 66.3 + - - +
94A GLU* 3.4 12.4 - - - +
120A ILE* 2.8 57.6 + - + +
122A HIS* 5.1 2.2 - - + -
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Residues in contact with VAL 93 (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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18A CYS 3.6 2.1 - - - +
19A ASN* 3.6 0.9 - - - -
20A GLY* 2.8 36.5 + - - -
70A THR* 3.9 17.8 - - + +
73A VAL* 4.5 7.2 - - + -
74A MSE 3.5 31.4 - - + +
77A ILE* 4.4 7.2 - - + -
91A LEU* 4.0 15.9 - - + -
92A ASP* 1.3 82.7 + - - +
94A GLU* 1.3 63.5 + - - +
95A CYS* 5.2 1.1 - - + -
117A ILE* 3.6 29.6 - - + -
118A ASP 3.4 3.6 - - - +
119A ILE* 4.3 13.0 - - + -
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Residues in contact with GLU 94 (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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18A CYS 3.3 5.8 - - - +
19A ASN* 3.1 24.7 - - + +
92A ASP* 3.4 8.3 - - - +
93A VAL* 1.3 73.2 - - - +
95A CYS* 1.3 59.9 + - - +
116A GLU 3.9 0.9 - - - +
117A ILE* 3.4 2.9 - - - +
118A ASP* 2.8 56.8 + - + +
120A ILE* 4.1 18.4 - - + +
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Residues in contact with CYS 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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17A THR* 3.1 6.9 - - - -
18A CYS 2.8 35.9 + - - +
66A ILE* 3.7 14.0 - - + +
69A LEU* 4.0 17.5 - - - -
70A THR* 3.4 26.0 - - + +
93A VAL* 5.2 1.3 - - + -
94A GLU* 1.3 74.3 - - - +
96A ARG* 1.3 63.0 + - - +
97A VAL* 3.8 24.5 - - - -
115A PHE* 5.6 0.4 - - - -
116A GLU 3.2 10.8 - - - +
117A ILE* 4.1 11.9 - - + -
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Residues in contact with ARG 96 (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 GLU* 4.9 4.8 + - - -
15A VAL* 3.8 23.0 - - + +
16A PHE 3.4 9.4 - - - +
17A THR* 3.9 15.6 - - + +
36A LYS* 5.6 4.2 - - - +
95A CYS* 1.3 73.1 - - - +
97A VAL* 1.3 66.3 + - - +
98A VAL* 3.5 29.4 - - + +
114A SER* 3.9 4.4 + - - +
115A PHE* 3.6 1.9 - - - -
116A GLU* 2.9 64.5 + - + +
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Residues in contact with VAL 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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15A VAL* 3.4 3.8 - - - +
16A PHE 2.9 32.7 + - - +
65A PHE* 4.7 3.1 - - + -
66A ILE* 3.8 22.7 - - + -
69A LEU* 4.5 2.5 - - + -
95A CYS* 3.8 11.0 - - - -
96A ARG* 1.3 78.4 - - - +
98A VAL* 1.3 67.3 + - - +
99A TRP* 3.5 42.2 - - + -
114A SER 3.4 7.9 - - - +
115A PHE* 3.6 40.4 - - + -
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Residues in contact with VAL 98 (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 GLU* 3.6 32.3 - - + +
14A VAL 3.4 6.3 - - - +
15A VAL* 4.0 6.5 - - + -
96A ARG* 3.5 36.3 - - + +
97A VAL* 1.3 80.5 - - - +
99A TRP* 1.3 66.6 + - - +
112A PRO* 3.8 1.2 - - - +
113A LYS* 2.8 45.0 + - + -
114A SER* 3.0 34.5 + - - +
115A PHE* 5.6 0.2 - - - -
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Residues in contact with TRP 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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13A GLU* 3.2 8.3 - - - +
14A VAL* 2.9 47.9 + - + +
16A PHE* 4.0 18.8 - + + -
62A LEU* 3.7 46.5 - - + +
65A PHE* 3.8 28.0 - + - -
66A ILE* 5.4 1.3 - - + -
97A VAL* 3.5 41.3 - - + +
98A VAL* 1.3 78.1 - - - +
100A ASP* 1.3 66.1 + - - +
110A THR* 5.8 4.7 - - - -
111A GLY 3.3 11.9 - - - +
112A PRO* 3.7 27.9 - - + +
113A LYS* 4.0 1.6 - - - +
115A PHE* 5.1 3.6 - + - -
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Residues in contact with ASP 100 (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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11A ARG* 5.1 4.3 - - + +
12A ALA 3.1 19.3 - - - +
13A GLU* 4.3 6.1 - - + +
14A VAL* 4.8 2.2 - - - +
99A TRP* 1.3 76.5 - - - +
101A TRP* 1.3 65.6 + - - +
110A THR* 3.2 5.2 - - - -
111A GLY* 2.9 41.7 + - - +
112A PRO 4.9 1.9 - - - +
113A LYS* 4.0 27.2 + - + +
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Residues in contact with TRP 101 (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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12A ALA* 3.0 56.6 + - + +
13A GLU 3.6 23.8 - - - -
14A VAL* 4.0 21.8 - - + -
37A PRO* 4.4 15.9 - - + -
100A ASP* 1.3 78.7 - - - +
102A ALA* 1.3 71.7 + - - +
103A LYS* 5.3 0.2 - - - -
108A TYR* 4.0 24.5 - + + -
109A GLU 3.2 11.4 - - - +
110A THR* 4.1 12.6 - - + -
173A GOL 3.7 25.1 + - - -
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Residues in contact with ALA 102 (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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101A TRP* 1.3 83.2 - - - +
103A LYS* 1.3 67.3 + - - +
108A TYR* 3.3 2.4 - - - -
109A GLU* 2.9 35.1 + - + +
173A GOL 3.7 9.6 - - - +
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Residues in contact with LYS 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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101A TRP* 5.3 0.4 - - - -
102A ALA* 1.3 78.5 - - - +
104A ALA* 1.3 62.1 + - - +
105A GLY* 2.7 39.6 + - - +
107A VAL 3.7 7.0 - - - +
108A TYR* 4.4 2.5 - - - +
173A GOL 3.1 35.9 + - - +
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Residues in contact with ALA 104 (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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102A ALA 3.5 0.4 + - - +
103A LYS* 1.3 74.8 - - - +
105A GLY* 1.3 63.8 + - - +
106A PRO* 3.2 4.9 - - - +
107A VAL* 2.7 30.2 + - + +
108A TYR 4.3 0.9 - - - -
109A GLU* 3.5 43.3 - - + +
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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