Contacts of the strand formed by residues 76 - 89 (chain A) in PDB entry 2JXP
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 76 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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65A ILE* 3.4 8.4 - - - +
66A LEU* 2.8 41.8 + - + +
67A SER* 3.4 6.9 + - - +
75A ARG* 1.3 131.5 + - - +
77A PHE* 1.3 60.5 + - - +
106A ILE* 3.6 30.7 - - + -
107A LEU 3.3 5.6 - - - +
108A PRO* 4.7 8.0 - - + +
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Residues in contact with PHE 77 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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63A LYS* 3.5 44.6 - - + -
64A ARG* 3.3 35.7 - - - -
65A ILE* 3.7 24.9 - - + -
66A LEU* 4.3 0.9 - - - -
74A VAL* 3.9 24.9 - - + -
76A GLU* 1.3 72.7 - - - +
78A GLU* 1.3 59.9 + - - +
79A LEU* 3.2 5.1 + - - +
105A ARG 3.4 0.3 - - - +
106A ILE* 4.1 0.6 - - - -
107A LEU* 2.7 59.2 + - + +
109A PHE* 5.4 6.7 - + + -
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Residues in contact with GLU 78 (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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63A LYS* 3.5 0.5 - - - -
64A ARG* 2.6 80.7 + - + +
65A ILE 5.1 1.4 - - - +
66A LEU* 3.7 40.5 - - + +
77A PHE* 1.3 67.6 - - - +
79A LEU* 1.3 59.5 + - - +
80A VAL* 3.2 8.8 + - + +
104A THR* 4.2 31.8 + - + +
105A ARG 3.8 4.0 - - - +
106A ILE* 5.9 1.6 - - + -
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Residues in contact with LEU 79 (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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61A ARG* 3.4 29.2 - - - +
62A GLU 3.6 4.9 - - - -
63A LYS* 3.5 23.1 - - + -
77A PHE* 3.8 7.0 - - + +
78A GLU* 1.3 67.8 - - - +
80A VAL* 1.3 59.8 + - - +
81A TYR 3.7 0.5 + - - -
103A LEU 3.4 3.3 - - - +
104A THR* 3.2 5.9 - - - -
105A ARG* 2.9 56.7 + - + +
107A LEU* 3.9 17.9 - - + -
120A GLU 5.3 0.2 - - - +
121A GLU* 3.4 20.6 - - - +
124A LEU* 3.9 27.1 - - + -
125A TYR 5.5 0.4 - - - +
128A MET* 3.9 7.6 - - + +
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Residues in contact with VAL 80 (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 ILE 3.5 3.1 - - - +
61A ARG* 4.4 0.9 - - - -
62A GLU* 3.0 63.5 + - + +
64A ARG* 4.2 30.3 - - - +
78A GLU* 3.2 8.0 + - + +
79A LEU* 1.3 71.6 - - - +
81A TYR* 1.3 66.5 + - - +
82A ARG* 4.6 15.9 - - + +
103A LEU 3.7 3.1 - - - +
104A THR* 4.0 19.7 - - + -
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Residues in contact with TYR 81 (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 ILE* 4.2 11.3 - - - +
59A ALA* 3.5 37.9 - - - +
60A ILE 3.3 17.3 - - - -
61A ARG* 3.5 13.5 - - + +
79A LEU 3.7 0.4 + - - -
80A VAL* 1.3 73.1 - - - +
82A ARG* 1.3 59.8 + - - +
83A VAL* 3.4 24.9 + - + +
101A ILE 3.5 15.6 - - - +
102A ARG* 4.8 0.2 - - - -
103A LEU* 2.8 29.1 + - + +
128A MET* 3.4 39.3 - - + -
129A GLN* 2.9 37.8 + - - -
132A ALA* 3.6 16.4 - - + -
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Residues in contact with ARG 82 (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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58A HIS* 3.6 3.5 - - + +
59A ALA* 3.1 5.4 + - - -
60A ILE* 2.9 43.4 + - + +
80A VAL* 4.0 16.7 - - + +
81A TYR* 1.3 73.4 - - - +
83A VAL* 1.3 65.0 + - - +
84A ALA 4.3 0.2 - - - -
100A GLU* 2.7 45.7 + - - +
101A ILE 4.1 6.6 + - - -
102A ARG* 4.0 16.2 - - - +
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Residues in contact with VAL 83 (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 ILE* 4.6 5.2 - - + -
56A ILE* 5.1 3.4 - - + -
58A HIS 3.4 6.7 - - - +
59A ALA* 4.4 6.5 - - + -
81A TYR* 3.4 46.2 - - + +
82A ARG* 1.3 77.1 + - - +
84A ALA* 1.3 67.4 + - - +
85A ALA* 5.3 2.5 - - + +
99A GLN 4.5 0.2 - - - +
100A GLU* 3.5 6.2 - - - +
101A ILE* 3.0 62.8 + - + +
132A ALA* 4.3 9.0 - - + -
136A ILE* 4.4 14.8 - - + -
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Residues in contact with ALA 84 (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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56A ILE* 3.7 2.1 - - - +
57A VAL* 2.8 41.7 + - + -
58A HIS* 2.9 24.5 + - + +
82A ARG* 4.3 0.9 - - - -
83A VAL* 1.3 76.3 - - - +
85A ALA* 1.3 56.4 + - - +
99A GLN 4.5 4.9 - - - -
100A GLU* 4.9 5.2 - - + +
154A HIS* 5.2 17.0 - - + -
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Residues in contact with ALA 85 (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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54A ILE* 5.9 2.5 - - + -
55A GLN 3.1 15.5 - - - +
56A ILE* 3.9 9.4 - - + -
57A VAL* 3.8 8.0 - - - +
83A VAL* 5.4 2.7 - - + -
84A ALA* 1.3 76.2 - - - +
86A ARG* 1.3 70.3 + - - +
98A LEU* 2.9 45.0 + - + +
99A GLN 4.2 6.6 + - - +
136A ILE* 5.2 12.1 - - + -
154A HIS* 5.8 2.5 + - - -
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Residues in contact with ARG 86 (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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54A ILE* 4.1 3.8 - - - +
55A GLN* 2.8 54.2 + - - +
57A VAL* 4.4 10.2 - - + +
85A ALA* 1.3 81.6 - - - +
87A LEU* 1.3 60.1 + - - +
88A LEU* 3.5 17.5 - - + -
94A GLU* 3.1 43.6 + - + +
96A ALA 4.4 1.8 - - - +
97A SER* 3.7 28.5 + - - +
98A LEU* 3.6 11.8 - - - +
154A HIS* 5.3 13.3 + - - +
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Residues in contact with LEU 87 (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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14A PHE* 5.5 5.4 - - + -
52A ALA* 5.3 9.4 - - + -
53A ILE 4.0 5.4 - - - +
54A ILE* 5.4 5.4 - - + -
86A ARG* 1.3 74.2 - - - +
88A LEU* 1.3 69.6 + - - +
95A LEU* 4.1 1.9 + - - +
96A ALA* 2.8 50.7 + - + +
98A LEU* 3.9 10.9 - - + +
139A GLN 5.0 0.2 - - - -
140A VAL* 3.8 39.7 - - + +
143A PHE* 3.7 36.8 - - + -
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Residues in contact with LEU 88 (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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52A ALA* 4.0 6.1 - - - +
53A ILE* 2.9 36.2 + - + +
55A GLN* 3.6 25.1 - - + -
86A ARG* 3.5 37.5 - - + -
87A LEU* 1.3 80.0 - - - +
89A ASP* 1.3 67.9 + - - +
92A ASN* 3.3 34.8 - - + +
93A ALA 3.3 7.0 - - - +
94A GLU* 3.9 20.2 - - + +
95A LEU* 5.2 1.3 - - - -
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Residues in contact with ASP 89 (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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51A GLU 4.5 5.0 - - - +
52A ALA* 4.8 2.0 - - - +
53A ILE* 3.3 10.7 - - - +
88A LEU* 1.3 76.4 - - - +
90A ALA* 1.3 69.2 + - - +
91A HIS* 3.0 30.2 + - - +
92A ASN 2.8 18.9 + - - -
93A ALA* 2.8 27.0 + - + +
95A LEU* 3.8 18.0 - - + +
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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