Contacts of the strand formed by residues 84 - 94 (chain A) in PDB entry 2E6J
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 GLY 84 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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53A LEU* 5.4 0.5 - - - +
82A ILE* 4.3 1.0 - - - +
83A LEU* 1.3 79.8 - - - +
85A ASN* 1.3 69.8 + - - +
86A PHE* 3.8 7.8 + - - +
108A CYS* 5.2 0.4 - - - -
109A VAL* 2.7 29.5 + - - +
110A ILE* 6.1 0.4 - - - -
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Residues in contact with ASN 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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83A LEU 5.0 0.2 - - - +
84A GLY* 1.3 78.0 - - - +
86A PHE* 1.3 62.3 + - - +
107A GLY 3.7 8.1 - - - +
108A CYS* 3.6 26.0 - - - -
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Residues in contact with PHE 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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19A ILE* 4.2 1.8 - - + -
53A LEU* 3.4 40.6 - - + -
57A PHE* 3.4 25.1 - + - -
78A PHE* 3.0 41.1 - + - -
84A GLY 4.0 4.9 - - - +
85A ASN* 1.3 79.2 - - - +
87A GLU* 1.3 62.0 + - - +
88A GLU* 4.3 10.8 - - + +
105A ILE* 4.2 8.7 - - + +
106A ARG* 4.2 2.4 - - - +
107A GLY* 3.3 45.3 + - - +
108A CYS 4.2 0.2 - - - -
109A VAL* 3.5 17.9 - - + -
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Residues in contact with GLU 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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86A PHE* 1.3 75.7 - - - +
88A GLU* 1.3 73.7 + - - +
89A GLU* 4.6 13.3 - - - +
104A THR* 4.5 21.8 - - + +
105A ILE 4.4 4.0 - - - +
106A ARG* 5.5 7.3 - - + +
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Residues in contact with GLU 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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49A PRO* 4.6 5.0 - - + +
50A THR* 5.3 0.5 + - - -
51A SER* 2.9 41.1 + - - -
53A LEU* 3.7 13.0 - - - +
54A GLY* 3.4 32.9 + - - +
57A PHE* 5.1 1.6 - - + -
86A PHE* 4.2 14.4 - - + +
87A GLU* 1.3 82.5 + - - +
89A GLU* 1.3 73.4 + - - +
90A PHE* 4.4 16.2 - - + -
104A THR* 3.7 3.8 - - - +
105A ILE* 3.5 29.9 + - + +
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Residues in contact with GLU 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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49A PRO* 5.2 8.7 - - - +
87A GLU* 4.6 13.4 - - + +
88A GLU* 1.3 85.2 + - - +
90A PHE* 1.3 66.5 + - - +
91A LEU* 4.4 5.2 + - + +
102A LYS* 4.0 31.4 + - + +
103A LEU 3.6 5.2 - - - +
104A THR* 4.0 23.1 - - + +
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Residues in contact with PHE 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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46A MET* 4.4 15.7 - - + -
47A THR 4.6 8.7 - - - +
49A PRO* 4.1 22.9 - - + -
54A GLY 3.8 17.3 - - - -
57A PHE* 3.7 21.8 - + + -
59A PHE* 3.1 46.7 - + + -
88A GLU* 4.4 19.5 - - + -
89A GLU* 1.3 77.4 - - - +
91A LEU* 1.3 63.5 + - - +
92A VAL* 5.6 0.2 - - - -
101A VAL 3.7 1.3 - - - +
102A LYS* 3.4 3.8 - - - +
103A LEU* 2.8 46.9 + - + +
105A ILE* 3.6 26.0 - - + -
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Residues in contact with LEU 91 (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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46A MET* 3.8 5.0 - - - +
47A THR* 3.2 42.8 + - + +
89A GLU* 4.4 5.1 + - + +
90A PHE* 1.3 85.0 - - - +
92A VAL* 1.3 68.0 + - - +
93A ASN* 4.1 1.6 - - - +
100A PRO* 4.1 23.3 - - + -
101A VAL 4.0 2.2 - - - -
102A LYS* 3.4 41.5 - - + +
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Residues in contact with VAL 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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10A ILE* 5.5 0.2 - - + -
12A PHE* 4.1 18.2 - - + -
34A LEU* 5.1 7.9 - - + -
44A PHE* 3.9 20.6 - - + -
45A ASN 3.0 26.0 - - - +
46A MET* 3.5 23.1 - - + -
90A PHE 5.6 0.4 - - - -
91A LEU* 1.3 77.0 - - - +
93A ASN* 1.3 64.5 + - - +
94A VAL* 3.4 9.9 + - + +
100A PRO* 2.9 30.1 - - - +
101A VAL* 3.8 27.3 + - + +
103A LEU* 6.2 0.2 - - + -
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Residues in contact with ASN 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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43A LEU 3.9 0.5 - - - +
44A PHE* 3.3 4.9 - - - -
45A ASN* 2.6 83.0 + - + +
46A MET 3.7 0.2 - - - -
47A THR* 2.6 31.9 + - - +
91A LEU* 5.7 1.1 - - - +
92A VAL* 1.3 70.6 - - - +
94A VAL* 1.3 58.9 + - - +
95A ASN 4.4 0.2 + - - -
100A PRO* 4.5 5.5 - - - +
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Residues in contact with VAL 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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8A PRO* 5.0 4.5 - - + -
9A LYS* 5.6 4.7 - - + -
10A ILE* 3.6 38.4 - - + -
42A ALA* 5.5 2.9 - - + -
43A LEU 3.3 17.9 - - - +
44A PHE* 4.5 1.3 - - - -
92A VAL* 3.4 21.4 + - + +
93A ASN* 1.3 79.6 - - - +
95A ASN* 1.3 71.9 + - - +
96A GLY 3.2 3.5 + - - -
97A SER* 3.3 40.2 + - - +
100A PRO* 5.2 1.6 - - + +
101A VAL* 5.2 0.7 - - + -
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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