Contacts of the strand formed by residues 89 - 103 (chain A) in PDB entry 1JPY
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 ASN 89 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75A LEU* 3.4 22.4 + - + +
77A CYS* 3.6 5.6 - - - -
86A ILE* 4.3 7.5 + - - +
88A MET* 1.3 84.8 + - - +
90A SER* 1.3 61.1 + - - +
91A VAL* 3.5 16.3 + - + -
124A CYS* 3.3 4.0 - - - -
125A VAL* 2.8 50.3 + - + +
127A PRO* 3.5 30.3 - - - +
128A VAL 5.0 0.2 + - - -
47B ARG* 5.5 0.7 + - - -
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Residues in contact with SER 90 (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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50A SER* 2.7 35.0 - - - -
51A PRO* 4.5 1.4 + - - +
72A CYS* 3.9 17.0 - - - +
74A ASN* 3.1 28.9 + - - +
75A LEU* 2.8 14.1 + - - +
76A GLY 3.1 15.3 + - - -
77A CYS* 4.0 1.3 - - - -
89A ASN* 1.3 70.6 - - - +
91A VAL* 1.3 61.7 + - - +
92A PRO* 4.6 0.7 - - - +
123A THR 3.7 5.2 - - - -
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Residues in contact with VAL 91 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72A CYS* 3.6 3.6 - - - -
89A ASN* 4.0 10.8 - - + -
90A SER* 1.3 79.3 - - - +
92A PRO* 1.3 70.4 - - + +
122A CYS* 3.3 1.7 - - - -
123A THR* 3.1 33.1 + - + +
125A VAL* 3.5 34.1 - - + -
41B SER* 3.8 18.6 - - - +
44B ILE* 3.8 26.2 - - + -
47B ARG* 5.5 0.2 - - - +
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Residues in contact with PRO 92 (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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72A CYS* 3.6 15.9 - - - +
90A SER 4.6 0.7 - - - +
91A VAL* 1.3 92.3 - - + +
93A ILE* 1.3 61.7 + - - +
94A GLN* 4.0 2.2 - - + -
119A THR* 3.8 28.0 - - + +
121A GLY 3.6 6.3 - - - +
39B SER 5.7 4.9 - - - +
40B MET* 3.6 18.2 - - - +
41B SER 5.3 0.3 + - - -
44B ILE* 3.8 8.1 - - - +
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Residues in contact with ILE 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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92A PRO* 1.3 77.4 - - - +
94A GLN* 1.3 59.5 + - - +
119A THR* 3.4 3.3 - - - -
120A VAL* 3.0 29.4 + - + +
121A GLY 2.7 14.9 + - - +
122A CYS 4.0 4.3 - - - -
123A THR* 3.9 25.6 - - - +
40B MET* 3.7 12.8 - - - -
44B ILE* 4.2 14.8 - - + -
52B TRP* 4.1 13.9 - - + -
93B ILE* 3.6 29.6 - - + -
120B VAL* 3.2 41.7 - - + +
121B GLY 4.6 1.3 - - - -
122B CYS 4.2 7.9 - - - +
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Residues in contact with GLN 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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92A PRO* 4.0 2.4 - - + -
93A ILE* 1.3 72.5 - - - +
95A GLN* 1.3 62.1 + - - +
117A LEU* 3.4 36.8 + - + +
118A VAL 3.3 9.2 - - - +
119A THR* 3.4 23.9 + - - +
37B ARG 4.5 0.2 - - - +
38B VAL* 3.5 30.3 - - + +
39B SER* 3.2 29.8 + - - +
40B MET* 3.3 21.5 - - + +
120B VAL* 4.2 6.7 - - - +
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Residues in contact with GLN 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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93A ILE 4.2 0.4 + - - -
94A GLN* 1.3 75.7 - - - +
96A GLU* 1.3 84.1 + - - +
97A THR* 3.5 2.3 + - - +
117A LEU* 3.4 4.1 - - - -
118A VAL* 2.7 40.7 + - + +
120A VAL* 4.0 11.9 - - + -
38B VAL* 5.5 0.2 - - - -
67B VAL* 5.8 1.6 - - - +
68B VAL* 4.8 11.8 + - - +
95B GLN* 4.6 12.3 - - + -
97B THR* 6.0 2.7 - - - -
118B VAL* 3.9 23.1 - - + +
120B VAL* 3.1 45.5 - - + +
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Residues in contact with GLU 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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95A GLN* 1.3 93.3 + - - +
97A THR* 1.3 63.0 + - - +
115A LYS* 2.8 45.2 + - + +
116A VAL 4.9 0.2 - - - +
117A LEU* 3.6 23.4 - - + +
36B GLN 3.8 6.2 - - - +
37B ARG* 4.4 7.4 + - - -
38B VAL* 4.3 20.8 + - + +
97B THR* 4.5 3.5 + - - +
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Residues in contact with THR 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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67A VAL* 5.6 0.7 - - + -
95A GLN* 4.7 1.6 - - - -
96A GLU* 1.3 76.2 - - - +
98A LEU* 1.3 76.8 + - - +
99A VAL* 4.5 6.8 - - + +
115A LYS* 3.2 10.6 - - - +
116A VAL* 2.8 70.5 + - + +
118A VAL* 3.5 16.2 - - + -
95B GLN* 5.3 9.6 - - - +
96B GLU 4.7 0.9 + - - -
97B THR* 2.6 28.5 + - - -
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Residues in contact with LEU 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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64A PRO* 4.8 0.9 - - - +
97A THR* 1.3 88.0 + - - +
99A VAL* 1.3 66.4 + - - +
113A LEU* 4.6 19.5 - - + -
114A GLU 3.3 15.9 - - - +
115A LYS* 3.9 15.0 - - + -
31B ILE* 4.9 4.3 - - + -
63B TYR* 3.8 45.8 - - + +
64B PRO* 4.3 7.0 - - + -
97B THR* 3.9 2.0 + - - -
98B LEU* 3.2 45.4 + - + +
99B VAL* 4.3 3.8 - - - -
100B VAL* 4.6 8.7 - - + +
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Residues in contact with VAL 99 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62A ARG* 3.7 28.3 - - + -
63A TYR 3.3 11.0 - - - +
64A PRO* 4.1 13.5 - - + -
67A VAL* 4.6 8.5 - - + -
97A THR* 4.5 8.1 - - + +
98A LEU* 1.3 80.4 - - - +
100A VAL* 1.3 63.7 + - - +
113A LEU* 3.7 3.7 - - - +
114A GLU* 2.7 53.5 + - + +
116A VAL* 3.5 28.0 - - + -
98B LEU* 4.5 0.9 - - - -
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Residues in contact with VAL 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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27A LEU* 5.5 2.7 - - + -
62A ARG* 3.2 6.9 - - - +
63A TYR* 2.7 53.7 + - + +
99A VAL* 1.3 76.2 - - - +
101A ARG* 1.3 63.4 + - - +
111A PHE* 3.7 31.0 - - + -
112A GLN 3.8 11.0 - - - +
113A LEU* 4.7 9.2 - - + +
10B PHE* 3.9 2.5 - - + -
11B PHE* 4.0 15.3 - - + -
27B LEU* 5.8 0.9 - - + -
98B LEU* 4.4 5.2 - - + -
113B LEU* 3.6 36.1 - - + -
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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
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59A ASP* 2.6 29.8 + - - +
61A ASN* 3.2 29.0 + - - +
62A ARG* 3.4 27.7 - - - +
99A VAL 3.9 0.6 + - - -
100A VAL* 1.3 76.1 - - - +
102A ARG* 1.3 68.8 + - - +
103A LYS* 3.8 9.2 + - + +
111A PHE* 3.5 6.1 - - - +
112A GLN* 2.8 36.4 + - + +
114A GLU* 2.7 31.8 + - + +
10B PHE* 4.4 0.2 - - - -
32B ILE* 4.3 21.1 - - + -
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Residues in contact with ARG 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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60A PRO 5.1 1.1 - - - -
61A ASN* 2.7 46.7 + - + +
101A ARG* 1.3 75.6 - - - +
103A LYS* 1.3 63.6 + - - +
104A HIS 3.4 22.7 + - - +
105A GLN* 4.5 4.2 - - - +
106A GLY* 4.5 11.5 + - - +
109A VAL* 3.3 27.2 - - + +
110A SER 3.8 2.2 - - - -
111A PHE* 3.7 16.4 - - + -
9B THR 5.3 3.2 + - - -
10B PHE* 3.4 46.9 + - + +
12B GLN 4.1 11.3 + - - -
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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 ARG* 4.0 16.8 - - + +
102A ARG* 1.3 78.5 - - - +
104A HIS* 1.3 87.4 + - + +
109A VAL* 3.3 4.7 - - - +
110A SER* 2.7 48.5 + - - +
112A GLN* 2.9 36.1 + - + +
28B ASP* 2.7 30.1 + - - +
32B ILE* 5.6 1.8 - - + -
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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