Contacts of the strand formed by residues 88 - 97 (chain E) in PDB entry 3V5I
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 VAL 88 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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48E LEU* 4.1 9.0 - - + -
60E ILE* 3.5 18.2 - - + +
62E LEU* 3.9 25.6 - - + -
81E ILE* 3.8 33.0 - - + +
84E ILE* 4.0 26.7 - - + -
86E PRO 3.6 2.4 + - - +
87E ASP* 1.3 77.8 - - - +
89E GLN* 1.3 73.0 + - - +
90E THR* 4.5 4.0 - - + -
107E GLY* 3.4 2.9 - - - -
108E ALA* 2.9 30.1 + - - +
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Residues in contact with GLN 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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59E ASP* 3.6 19.2 + - - +
60E ILE 2.7 17.2 + - - +
61E TYR* 3.5 37.6 + - + -
62E LEU* 2.8 30.8 + - - +
88E VAL* 1.3 73.8 - - - +
90E THR* 1.3 61.9 + - - +
91E ILE* 4.9 3.3 - - + +
111E LYS* 3.2 46.7 - - + +
113E PHE* 3.2 25.2 - - + -
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Residues in contact with THR 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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62E LEU* 3.3 17.5 - - + +
64E ILE* 4.1 12.8 - - + -
81E ILE* 5.4 1.8 - - + -
88E VAL* 3.8 4.6 + - + +
89E GLN* 1.3 78.4 - - - +
91E ILE* 1.3 60.7 + - - +
103E LEU 3.8 14.1 - - - +
104E LEU* 2.7 31.2 + - - +
106E ALA 4.8 0.2 - - - -
107E GLY* 3.6 18.6 - - - -
111E LYS 3.1 4.2 + - - +
112E ARG* 3.4 13.7 - - - +
113E PHE* 2.7 33.5 + - - -
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Residues in contact with ILE 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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61E TYR* 4.3 25.6 - - + -
62E LEU 2.9 11.4 + - - +
63E TYR* 3.3 55.1 - - + +
64E ILE* 2.8 26.2 + - - -
89E GLN* 4.9 3.6 - - + +
90E THR* 1.3 80.2 - - - +
92E CYS* 1.3 62.2 + - - +
93E ILE* 3.5 5.8 + - + -
104E LEU* 4.3 2.5 - - - -
113E PHE* 3.5 24.0 - - + -
115E LEU* 4.4 10.1 - - + -
190E MET* 4.0 24.7 - - + -
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Residues in contact with CYS 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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64E ILE* 3.4 8.1 - - - +
91E ILE* 1.3 73.1 - - - +
93E ILE* 1.3 64.8 + - - +
95E MET 4.1 2.7 - - - -
96E ALA* 3.6 35.4 - - + -
104E LEU* 3.6 28.8 - - + +
113E PHE 3.0 11.9 + - - +
114E ALA* 4.0 4.9 - - + -
115E LEU* 3.1 25.3 + - - +
118E ALA* 3.5 18.9 - - - +
119E GLU 3.9 7.0 - - - -
120E VAL* 4.5 2.5 - - - -
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Residues in contact with ILE 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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42D ASN* 5.3 4.3 - - - +
45D VAL* 4.0 28.9 - - + -
76D ALA* 4.1 22.0 - - + -
79D ASP* 6.1 0.2 - - - -
80D THR* 4.5 4.9 - - - +
31E MET* 4.5 8.7 - - + -
63E TYR* 4.1 27.8 - - + -
64E ILE 3.0 18.3 + - - +
65E ASN* 3.2 22.5 - - + +
91E ILE* 3.5 1.5 + - + -
92E CYS* 1.3 77.7 - - - +
94E GLY* 1.3 60.9 + - - +
95E MET 3.0 8.2 + - - -
115E LEU* 3.7 30.7 - - + -
118E ALA* 4.3 1.8 - - - -
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Residues in contact with GLY 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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72D THR* 3.2 33.2 - - - +
75D PHE* 4.5 4.9 - - - +
76D ALA* 3.7 14.0 - - - +
79D ASP* 5.6 1.6 + - - +
65E ASN* 3.9 4.0 - - - -
93E ILE* 1.3 69.1 - - - +
95E MET* 1.3 61.1 + - - +
117E ASN 4.4 1.7 - - - +
118E ALA* 3.3 11.5 - - - +
119E GLU* 2.9 25.6 + - - +
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Residues in contact with MET 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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72D THR* 3.7 27.4 - - + +
142D HIS* 4.5 3.4 - - + +
65E ASN* 3.1 11.3 + - - +
66E SER 2.9 31.1 + - - +
67E PRO* 5.2 3.1 - - + -
92E CYS* 4.1 3.8 - - - -
93E ILE 3.0 5.3 + - - -
94E GLY* 1.3 73.6 - - - +
96E ALA* 1.3 66.5 + - - +
97E ALA* 3.9 25.6 - - + +
119E GLU* 3.2 46.9 - - + +
121E MET* 4.3 7.0 - - + -
174E PHE* 3.9 23.8 - - + -
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Residues in contact with ALA 96 (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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64E ILE* 4.1 11.2 - - + -
66E SER 3.5 4.9 - - - +
92E CYS* 3.6 19.7 - - - -
95E MET* 1.3 73.4 - - - +
97E ALA* 1.3 60.6 + - - +
100E GLY 4.0 9.2 - - - +
101E SER* 3.2 28.4 - - - +
104E LEU* 4.1 10.8 - - + -
119E GLU 2.9 9.6 + - - +
120E VAL* 3.3 3.3 - - + -
121E MET 3.2 18.3 + - - -
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Residues in contact with ALA 97 (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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66E SER 3.0 8.3 + - - +
67E PRO* 3.5 26.2 - - + +
68E GLY* 3.5 1.2 - - - -
95E MET* 3.9 18.6 - - + -
96E ALA* 1.3 74.3 - - - +
98E ALA* 1.3 61.5 + - - +
99E MET 3.2 0.5 + - - -
100E GLY* 2.7 27.9 + - - -
121E MET* 3.4 27.1 - - + +
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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