Contacts of the strand formed by residues 84 - 103 (chain B) 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 GLU 84 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74B ASN* 3.3 16.2 + - + +
75B LEU* 3.2 13.5 + - - +
76B GLY* 2.7 33.3 + - - +
77B CYS 3.2 11.7 - - - +
78B ILE* 4.0 13.4 - - + +
79B ASN* 5.2 1.0 + - - -
82B GLY 4.2 0.4 + - - -
83B LYS* 1.3 77.8 - - - +
85B ASP* 1.3 65.6 + - - +
86B ILE* 3.9 16.0 + - + +
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Residues in contact with ASP 85 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77B CYS* 2.7 20.1 + - + +
79B ASN* 4.7 17.5 + - + +
83B LYS 4.6 3.6 - - - +
84B GLU* 1.3 77.5 - - - +
86B ILE* 1.3 57.3 + - - +
87B SER* 2.7 32.9 + - - -
88B MET* 2.9 32.2 + - + +
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Residues in contact with ILE 86 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75B LEU* 4.6 11.2 - - + -
76B GLY* 4.4 5.6 - - - +
84B GLU* 3.9 27.2 - - + +
85B ASP* 1.3 67.4 + - - +
87B SER* 1.3 59.7 + - - +
88B MET 2.9 12.8 + - - +
89B ASN* 4.1 10.0 + - - +
127B PRO* 5.3 1.2 - - - +
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Residues in contact with SER 87 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85B ASP* 2.7 26.0 + - - -
86B ILE* 1.3 75.9 - - - +
88B MET* 1.3 67.7 + - - +
127B PRO* 2.9 29.4 - - - +
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Residues in contact with MET 88 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49A THR* 3.3 33.9 - - + -
78A ILE 5.6 0.7 - - - +
79A ASN 6.6 0.7 - - - -
76B GLY* 2.9 25.3 - - - -
77B CYS* 3.8 15.9 - - + -
85B ASP* 2.9 20.1 + - + +
86B ILE 3.8 1.4 - - - -
87B SER* 1.3 94.5 - - - +
89B ASN* 1.3 65.2 + - - +
124B CYS* 3.7 8.7 - - - -
125B VAL 3.8 4.9 - - - +
126B THR* 3.8 29.2 - - + -
127B PRO* 4.7 0.2 - - - -
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Residues in contact with ASN 89 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47A ARG* 5.1 1.0 + - - -
75B LEU* 3.7 13.8 + - - +
76B GLY* 4.9 0.2 - - - -
77B CYS* 3.3 4.8 - - - -
86B ILE* 4.1 11.5 + - - +
88B MET* 1.3 80.6 + - - +
90B SER* 1.3 58.5 + - - +
91B VAL* 3.8 7.9 - - + -
124B CYS* 3.3 5.0 - - - -
125B VAL* 2.8 53.9 + - + +
127B PRO* 3.2 30.6 - - - +
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Residues in contact with SER 90 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50B SER* 2.9 29.8 - - - -
51B PRO 5.1 0.3 + - - -
72B CYS* 4.1 15.1 - - - +
74B ASN* 3.4 27.1 + - - +
75B LEU* 3.1 10.9 + - - +
76B GLY* 2.9 20.8 + - - -
77B CYS* 4.2 0.4 + - - -
89B ASN* 1.3 70.9 - - - +
91B VAL* 1.3 64.7 + - - +
92B PRO* 4.4 1.6 - - - +
123B THR 3.5 5.8 - - - -
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Residues in contact with VAL 91 (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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41A SER* 3.2 24.2 - - - +
44A ILE* 3.5 18.4 - - + -
72B CYS* 3.6 4.0 - - - -
89B ASN* 4.5 5.8 - - + -
90B SER* 1.3 79.3 - - - +
92B PRO* 1.3 72.7 - - + +
122B CYS* 3.3 1.9 - - - -
123B THR* 2.9 34.6 + - + +
125B VAL* 3.3 44.4 - - + -
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Residues in contact with PRO 92 (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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39A SER 5.9 2.5 - - - +
40A MET* 3.7 12.8 - - + +
41A SER* 5.3 0.6 + - - +
44A ILE* 3.6 14.6 - - - +
72B CYS* 3.6 17.0 - - - +
90B SER 4.4 1.1 - - - +
91B VAL* 1.3 92.9 - - + +
93B ILE* 1.3 60.1 + - - +
94B GLN* 4.1 3.8 - - + -
119B THR* 3.6 23.6 - - + +
121B GLY 3.7 6.1 - - - +
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Residues in contact with ILE 93 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40A MET* 3.5 11.2 - - + -
44A ILE* 4.4 8.3 - - + -
52A TRP* 3.7 30.5 - - + -
93A ILE* 3.6 30.1 - - + -
120A VAL* 3.2 37.0 - - + +
121A GLY* 4.2 6.1 - - - -
122A CYS 4.1 7.2 - - - +
92B PRO* 1.3 76.0 - - - +
94B GLN* 1.3 61.9 + - - +
119B THR* 3.4 2.8 - - - -
120B VAL* 2.9 29.4 + - + +
121B GLY 3.0 15.6 + - - +
123B THR* 4.4 9.9 - - + +
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Residues in contact with GLN 94 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38A VAL* 3.5 30.4 - - + +
39A SER* 3.1 32.4 + - - +
40A MET* 3.2 19.9 - - + +
120A VAL* 4.3 4.0 - - - +
92B PRO* 5.8 3.4 - - + -
93B ILE* 1.3 75.2 - - - +
95B GLN* 1.3 63.8 + - - +
96B GLU 4.3 0.2 + - - -
117B LEU* 3.4 36.2 - - + +
118B VAL 3.3 5.8 - - - +
119B THR* 3.7 23.1 + - + +
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Residues in contact with GLN 95 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38A VAL* 5.4 0.2 - - - -
67A VAL* 6.0 1.2 - - - +
68A VAL 5.6 0.2 - - - +
95A GLN* 4.6 13.7 - - + -
97A THR* 5.3 6.5 - - - +
118A VAL* 4.1 26.2 - - + +
120A VAL* 3.7 30.3 - - + +
93B ILE 4.1 0.2 + - - -
94B GLN* 1.3 76.2 - - - +
96B GLU* 1.3 83.1 + - - +
97B THR* 3.7 5.2 + - - -
117B LEU* 3.4 3.9 - - - -
118B VAL* 2.7 41.7 + - + +
120B VAL* 3.9 21.5 - - + -
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Residues in contact with GLU 96 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36A GLN 3.4 10.9 - - - +
37A ARG* 4.2 16.9 + - - +
38A VAL* 4.2 17.0 - - + +
97A THR* 4.7 1.2 + - - -
94B GLN 4.2 0.8 + - - -
95B GLN* 1.3 94.7 + - - +
97B THR* 1.3 60.9 + - - +
115B LYS* 2.5 50.6 + - + +
117B LEU* 3.5 15.4 - - + +
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Residues in contact with THR 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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95A GLN* 6.0 2.2 - - - -
96A GLU 4.5 3.5 + - - +
97A THR* 2.6 30.9 + - - -
67B VAL* 5.6 1.1 - - + -
95B GLN* 4.7 5.8 - - - -
96B GLU* 1.3 76.3 - - - +
98B LEU* 1.3 77.4 + - - +
99B VAL* 4.3 7.6 - - + -
115B LYS* 3.3 9.7 - - - +
116B VAL* 2.8 62.4 + - + +
118B VAL* 3.9 20.2 - - + -
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Residues in contact with LEU 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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31A ILE* 4.9 7.0 - - + -
63A TYR* 3.9 44.4 - - + +
64A PRO* 4.1 8.3 - - + -
97A THR* 4.0 1.4 + - - -
98A LEU* 3.2 45.3 + - + +
99A VAL* 4.5 0.2 - - - -
100A VAL* 4.4 11.0 - - + -
64B PRO* 4.9 0.5 - - - +
97B THR* 1.3 93.1 + - - +
99B VAL* 1.3 69.4 + - - +
113B LEU* 4.7 14.8 - - + -
114B GLU 3.4 13.0 - - - +
115B LYS* 4.2 14.1 - - + -
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Residues in contact with VAL 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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98A LEU* 4.3 3.1 - - - -
62B ARG* 3.8 23.3 - - + -
63B TYR 3.3 13.0 - - - +
64B PRO* 4.0 13.7 - - + -
67B VAL* 4.5 12.1 - - + -
97B THR* 4.3 7.4 - - + -
98B LEU* 1.3 82.0 - - - +
100B VAL* 1.3 64.2 + - - +
113B LEU* 3.6 4.2 - - - +
114B GLU* 2.8 48.9 + - + +
116B VAL* 3.4 32.8 - - + -
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Residues in contact with VAL 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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10A PHE* 3.9 2.6 - - + -
11A PHE* 3.7 23.1 - - + -
27A LEU* 6.0 0.4 - - + -
98A LEU* 4.7 4.7 - - + -
113A LEU* 3.5 40.2 - - + -
27B LEU* 5.4 2.5 - - + -
62B ARG* 3.4 3.3 - - - -
63B TYR* 2.7 43.2 + - + +
99B VAL* 1.3 75.7 - - - +
101B ARG* 1.3 64.4 + - - +
111B PHE* 3.7 31.4 - - + -
112B GLN 3.7 6.1 - - - +
113B LEU* 3.8 13.2 - - + -
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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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32A ILE* 4.2 19.3 - - + +
59B ASP* 2.9 36.0 + - - -
61B ASN* 3.5 18.5 + - + +
62B ARG* 3.7 22.8 - - - +
99B VAL 4.0 1.0 + - - -
100B VAL* 1.3 75.7 - - - +
102B ARG* 1.3 69.0 + - - +
103B LYS* 3.7 8.1 + - + -
111B PHE* 3.0 6.6 - - - +
112B GLN* 2.7 47.6 + - + +
114B GLU* 2.5 42.7 + - + +
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Residues in contact with ARG 102 (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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9A THR 5.3 0.6 + - - -
10A PHE* 2.7 62.4 + - + +
12A GLN 3.4 21.8 + - - -
13A LYS* 5.2 3.8 - - - +
14A PRO* 5.2 7.3 - - - +
60B PRO 4.8 3.1 - - - -
61B ASN* 3.0 40.4 + - - +
100B VAL 3.9 0.6 + - - -
101B ARG* 1.3 73.0 - - - +
103B LYS* 1.3 64.4 + - - +
104B HIS 4.2 6.3 + - - +
105B GLN* 6.2 0.2 - - - +
109B VAL* 4.0 18.0 - - + +
110B SER 3.6 3.8 - - - -
111B PHE* 3.9 15.4 - - + -
58X TRP* 5.3 7.4 - - - -
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Residues in contact with LYS 103 (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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28A ASP* 2.9 31.0 + - - +
32A ILE* 5.8 0.4 - - + -
101B ARG* 4.4 12.6 - - + +
102B ARG* 1.3 75.3 - - - +
104B HIS* 1.3 91.8 + - + +
109B VAL* 3.4 5.5 - - - +
110B SER* 2.6 39.6 + - - +
112B GLN* 3.1 41.5 + - + +
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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
------------------------------------------------------------
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