Contacts of the strand formed by residues 87 - 95 (chain E) in PDB entry 6NQN
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 TYR 87 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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65E ASN* 2.6 33.8 + - - -
66E ARG* 3.0 19.6 + - - +
78E TYR* 5.3 1.1 - + + -
79E PHE* 3.6 35.2 - + + -
82E SER* 4.0 11.7 - - - +
83E PHE* 4.0 26.0 - + - -
86E GLY* 1.3 74.8 - - - +
88E SER* 1.3 71.8 + - - +
89E TRP* 3.9 21.0 - + - -
107E ILE* 3.0 46.9 + - + +
177E TYR* 4.1 4.2 - + + -
178E LYS 3.3 18.4 - - - +
179E ALA* 3.7 9.9 - - - +
180E LYS* 4.0 7.9 - - - +
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Residues in contact with SER 88 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87E TYR* 1.3 80.3 - - - +
89E TRP* 1.3 66.7 + - - +
90E GLU* 5.2 3.5 + - - +
105E ASN 3.2 13.5 - - - -
106E ASP* 3.8 18.6 - - - -
178E LYS* 2.8 49.6 + - - +
180E LYS* 4.3 5.8 - - - +
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Residues in contact with TRP 89 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60E VAL* 3.7 36.6 - - + -
63E KZ4 2.7 33.2 + - - -
87E TYR* 3.9 22.7 - + - -
88E SER* 1.3 75.8 - - - +
90E GLU* 1.3 75.3 + - - +
91E ARG* 3.6 52.0 - - + -
103E ALA* 3.8 16.8 - - + -
104E THR* 3.3 6.9 - - - -
105E ASN* 2.9 56.4 + - + +
107E ILE* 4.1 4.0 - - + -
175E THR* 4.2 2.5 - - + -
176E THR 3.1 13.2 - - - +
177E TYR* 3.8 22.2 - + + -
178E LYS* 6.0 0.4 - - - -
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Residues in contact with GLU 90 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19B ASN* 3.1 33.8 - - - +
20B GLY* 5.5 0.2 - - - -
123B VAL* 3.9 11.7 - - + -
124B ASN* 2.9 37.6 + - - +
125B PHE 5.2 0.2 - - - +
88E SER* 5.2 4.5 + - - +
89E TRP* 1.3 80.5 - - - +
91E ARG* 1.3 61.1 + - - +
103E ALA 3.4 7.2 - - - +
104E THR* 4.2 11.2 - - + -
175E THR* 3.2 4.7 - - - +
176E THR* 2.8 35.1 + - - +
178E LYS* 2.8 38.2 + - + +
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Residues in contact with ARG 91 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123B VAL* 3.8 7.6 - - - +
124B ASN* 4.2 1.1 + - - +
59E THR* 2.8 42.6 + - - -
60E VAL* 4.0 2.6 - - - +
63E KZ4 2.7 28.2 + - - +
66E ARG* 3.7 11.9 - - - +
89E TRP* 3.6 38.6 - - + -
90E GLU* 1.3 78.5 - - - +
92E SER* 1.3 70.2 + - - +
93E MET* 3.7 26.1 - - + +
101E CYS 3.8 0.5 - - - +
102E ASN* 3.3 4.0 - - - -
103E ALA 2.8 38.6 + - - +
173E PHE* 4.0 13.9 - - - -
174E LYS 3.1 9.2 - - - +
175E THR* 2.9 26.7 + - - +
177E TYR* 5.0 0.2 - - - -
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Residues in contact with SER 92 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100B ILE* 3.6 26.2 - - - +
123B VAL* 4.3 1.6 - - - -
124B ASN* 3.7 11.5 - - - +
91E ARG* 1.3 76.1 - - - +
93E MET* 1.3 62.1 + - - +
94E ASN* 4.0 4.2 + - - +
100E ILE* 3.7 12.3 - - - +
101E CYS 3.5 3.1 - - - -
102E ASN* 3.1 18.0 + - - -
172E ASP 3.5 3.3 - - - +
173E PHE* 3.5 1.9 - - - -
174E LYS* 2.9 40.7 + - - +
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Residues in contact with MET 93 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56E ILE 4.6 8.5 - - - +
59E THR* 3.9 17.5 - - - -
60E VAL* 3.8 12.3 - - + -
91E ARG* 3.7 32.3 - - + +
92E SER* 1.3 73.2 + - - +
94E ASN* 1.3 59.4 + - - +
95E TYR* 3.6 16.2 - - + -
100E ILE* 3.4 5.2 - - - -
101E CYS* 2.8 59.7 + - + +
103E ALA* 3.8 27.4 - - + -
120E PHE* 4.1 2.2 - - + -
139E TRP* 6.0 0.2 - - - -
171E CYS* 3.8 14.1 - - - -
172E ASP 3.5 4.0 - - - -
173E PHE* 3.8 18.8 - - + -
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Residues in contact with ASN 94 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94B ASN* 4.2 18.8 - - - +
100B ILE* 6.1 0.4 - - - +
92E SER* 5.2 3.6 - - - +
93E MET* 1.3 70.7 - - - +
95E TYR* 1.3 73.5 + - - +
96E GLU* 4.9 0.2 - - - -
98E GLY* 5.0 1.2 - - - -
100E ILE* 3.1 30.6 - - + +
171E CYS* 3.5 2.1 - - - -
172E ASP* 2.8 47.4 + - + +
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Residues in contact with TYR 95 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56E ILE* 3.5 27.1 + - + +
93E MET* 3.6 19.3 - - + +
94E ASN* 1.3 84.2 - - - +
96E GLU* 1.3 66.3 + - - +
97E ASP* 3.2 2.9 - - - +
98E GLY* 3.0 13.2 + - - -
99E GLY 2.8 22.2 + - - +
101E CYS* 4.2 8.1 - - - -
125E PHE* 3.7 21.5 - + - -
139E TRP* 3.5 27.1 - + - -
161E LEU* 4.0 9.0 - - + -
169E TYR* 3.2 46.2 - + + +
170E ARG 3.4 6.1 - - - -
171E CYS* 3.5 32.9 - - + +
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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