Contacts of the strand formed by residues 93 - 98 (chain B) in PDB entry 3O75
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 93 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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105A SER* 5.1 1.2 + - - +
108A GLN* 2.9 49.5 + - - +
109A LEU* 3.6 30.7 - - + +
112A LEU* 3.6 25.0 - - + +
62B ARG 3.0 7.9 + - - +
63B THR* 3.1 14.1 - - + +
64B LEU* 2.6 34.6 + - - +
87B ALA* 5.2 0.7 - - - -
88B ARG* 5.2 10.3 - - - +
92B TYR* 1.3 77.9 + - - +
94B LEU* 1.3 56.2 + - - +
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Residues in contact with LEU 94 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96A ILE 3.9 1.6 - - - +
97A ALA* 3.7 22.2 - - - +
98A SER 5.2 0.3 + - - -
109A LEU* 5.3 0.5 - - - +
64B LEU* 3.2 31.9 - - + +
65B GLY 4.0 2.0 - - - +
66B PHE* 3.9 22.7 - - + -
80B ALA* 3.6 13.2 - - - +
83B LEU* 3.8 10.1 - - + -
84B GLU* 3.6 44.9 + - + +
87B ALA* 5.1 4.9 - - + -
92B TYR 4.3 0.6 + - - -
93B GLN* 1.3 78.0 - - - +
95B LEU* 1.3 64.3 + - - +
96B ILE* 3.9 23.1 - - + +
122B PHE* 4.5 7.4 - - + -
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Residues in contact with LEU 95 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95A LEU* 4.5 17.9 - - + -
96A ILE 3.7 1.1 - - - +
97A ALA* 4.6 2.2 - - + -
112A LEU* 3.7 27.4 - - + -
113A PHE* 4.1 30.3 - - + -
116A ARG* 3.6 38.6 - - - +
63B THR* 4.3 6.1 - - - +
64B LEU 2.8 11.8 + - - +
65B GLY* 3.4 2.9 - - - -
66B PHE 3.0 24.3 + - - -
94B LEU* 1.3 76.5 - - - +
96B ILE* 1.3 60.9 + - - +
113B PHE* 3.4 17.4 - - + -
116B ARG* 4.8 1.3 - - + -
118B CYS* 4.2 15.5 - - - -
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Residues in contact with ILE 96 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71A LEU* 3.8 28.3 - - + -
94A LEU 3.8 0.5 - - - +
95A LEU* 3.6 2.9 - - - -
96A ILE* 2.7 55.6 + - + +
97A ALA* 5.3 2.5 - - - -
98A SER 5.6 0.4 - - - +
66B PHE* 3.6 9.9 - - + +
68B LEU* 3.7 30.5 - - + -
71B LEU* 4.5 12.1 - - + -
80B ALA* 3.7 23.8 - - + -
84B GLU* 5.4 0.9 - - + -
94B LEU* 3.9 26.5 - - + +
95B LEU* 1.3 78.3 - - - +
97B ALA* 1.3 68.7 + - - +
113B PHE* 4.6 0.9 - - - -
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Residues in contact with ALA 97 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94A LEU 3.7 14.8 - - - +
95A LEU* 4.2 2.9 - - + -
96A ILE* 5.1 2.9 - - - -
66B PHE 3.0 8.7 + - - +
67B ILE* 3.4 2.1 - - - -
68B LEU* 2.9 27.8 + - - +
71B LEU* 5.5 0.4 - - - -
95B LEU 4.3 0.2 + - - -
96B ILE* 1.3 80.8 - - - +
98B SER* 1.3 61.0 + - - +
109B LEU* 3.6 31.6 - - + -
113B PHE* 4.0 17.0 - - + -
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Residues in contact with SER 98 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84A GLU* 2.6 29.8 + - - +
88A ARG* 2.8 22.7 + - - -
94A LEU 5.0 0.8 + - - -
96A ILE* 5.5 0.4 - - - +
68B LEU* 2.9 11.2 - - - -
69B PRO 3.4 11.6 + - - -
70B ASP* 4.1 1.7 + - - -
71B LEU* 3.8 25.0 + - - +
97B ALA* 1.3 75.1 - - - +
99B SER* 1.3 62.0 + - - +
100B ASP* 3.1 14.4 + - - -
109B LEU* 3.3 9.0 - - - +
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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