Contacts of the strand formed by residues 82 - 89 (chain A) in PDB entry 6EKK
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 GLN 82 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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4A ARG* 3.0 38.7 + - - +
5A ILE* 4.0 18.4 - - + +
6A LYS 4.9 2.6 + - - +
74A VAL* 3.8 17.3 - - + -
75A LEU 3.6 2.9 - - - -
76A THR* 4.7 5.4 - - - +
80A SER 4.1 5.4 - - - +
81A LYS* 1.3 79.7 - - - +
83A ARG* 1.3 61.9 + - - +
84A PHE* 3.9 26.3 - - + -
102A TYR* 3.3 20.4 - - - +
227A TYR* 3.3 30.5 - - - +
403A EDO 3.4 21.8 + - - -
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Residues in contact with ARG 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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14A GLU* 4.9 5.2 - - + -
46A VAL* 4.1 24.2 - - - +
74A VAL* 3.2 5.5 - - - -
75A LEU* 2.8 69.1 + - + +
76A THR 3.5 14.8 + - - -
77A ASP* 3.9 16.2 - - - +
81A LYS 4.0 0.4 + - - -
82A GLN* 1.3 71.7 - - - +
84A PHE* 1.3 62.1 + - - +
85A GLY 3.8 0.3 + - - -
100A LEU* 3.8 31.2 - - + +
101A SER 3.8 6.1 - - - +
102A TYR* 3.5 39.7 + - + -
39C THR* 2.8 29.3 + - - -
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Residues in contact with PHE 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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5A ILE* 3.5 33.7 - - + -
72A THR* 3.9 5.8 - - + -
73A PHE 3.5 2.5 - - - -
74A VAL* 3.5 24.5 - - + -
82A GLN* 3.9 27.8 - - + -
83A ARG* 1.3 71.9 - - - +
85A GLY* 1.3 60.0 + - - +
86A PHE* 3.4 26.7 + + + -
99A ILE 3.2 3.5 - - - +
100A LEU* 3.2 5.1 - - - -
101A SER 2.8 41.7 + - - +
102A TYR 4.0 10.8 - - - -
103A LEU 4.3 0.2 - - - -
104A PRO* 3.9 19.1 - - + -
106A PHE* 4.0 22.4 - + - -
212A HIS* 3.9 12.6 - + - -
227A TYR* 5.7 0.7 - + - -
405A EDO 5.2 4.3 - - - -
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Residues in contact with GLY 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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72A THR* 3.2 5.2 - - - -
73A PHE* 2.7 60.7 + - - -
83A ARG 3.8 1.8 + - - -
84A PHE* 1.3 70.3 - - - +
86A PHE* 1.3 64.2 + - - -
87A CYS* 3.3 7.4 + - - -
98A CYS* 4.1 5.4 - - - -
99A ILE 3.7 4.9 - - - -
100A LEU* 4.0 5.3 - - - +
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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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72A THR* 3.3 24.5 - - + -
84A PHE* 3.4 25.4 - + + -
85A GLY* 1.3 70.5 - - - -
87A CYS* 1.3 58.5 + - - +
98A CYS* 3.2 4.5 - - - -
99A ILE* 3.0 52.7 + - + +
101A SER* 4.1 5.2 - - - -
103A LEU 3.2 22.4 - - - -
104A PRO* 4.2 0.9 - - + -
105A TRP 3.8 9.0 - - - -
106A PHE* 3.6 40.6 - + - -
109A PHE* 3.3 37.7 - + + -
110A TYR* 4.3 7.6 - + + -
113A LEU* 3.4 9.7 - - + +
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Residues in contact with CYS 87 (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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54A CYS* 4.2 1.8 - - - -
70A ASN* 3.1 28.4 + - - +
71A PHE* 2.7 47.6 + - + +
73A PHE* 3.5 36.3 - - - -
85A GLY 3.6 5.2 - - - -
86A PHE* 1.3 75.1 - - - +
88A ARG* 1.3 60.6 + - - +
89A LEU 4.2 0.4 - - - -
96A CYS* 3.8 11.9 - - - -
97A PHE 3.3 2.7 - - - -
98A CYS* 3.9 13.2 - - - -
110A TYR* 4.0 3.2 - - - -
113A LEU* 3.8 3.1 - - - -
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Residues in contact with ARG 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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69A GLN* 3.4 38.0 - - + +
70A ASN* 3.6 10.3 - - - +
87A CYS* 1.3 73.3 - - - +
89A LEU* 1.3 64.1 + - - +
90A SER* 5.2 4.8 + - - +
96A CYS* 3.5 3.9 - - - -
97A PHE* 2.8 56.3 + - + +
113A LEU* 3.9 21.1 - - + -
114A ASN* 2.7 34.4 + - - +
117A ALA* 3.8 31.3 - - - +
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Residues in contact with LEU 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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54A CYS 4.1 4.0 - - - +
55A PHE* 3.8 19.3 - - + -
57A PHE* 4.2 14.6 - - + -
67A VAL* 5.1 4.9 - - - +
68A GLY 3.7 17.3 - - - +
69A GLN* 2.6 39.8 + - - +
71A PHE* 3.9 27.1 - - + -
88A ARG* 1.3 76.3 + - - +
90A SER* 1.3 67.1 + - - +
93A ALA* 4.2 12.1 - - - -
95A SER 3.5 15.7 - - - +
96A CYS* 3.8 15.7 - - + -
204A LEU* 4.0 15.9 - - + -
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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