Contacts of the strand formed by residues 93 - 101 (chain B) in PDB entry 2O38
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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99A ILE* 3.8 16.2 - - + -
100A ARG 3.2 4.7 - - - +
101A LYS* 3.4 29.8 + - - +
109A ALA* 3.3 5.3 - - - +
46B VAL* 3.5 33.9 - - + +
49B ARG* 4.8 1.2 + - - -
88B LEU* 3.0 24.1 + - + +
89B ASN* 2.9 25.6 + - - +
91B LEU* 2.9 22.1 + - + +
92B ASP* 1.3 87.4 + - - +
94B ASP* 1.3 59.9 + - - +
95B VAL* 4.2 0.9 - - - +
202B ACY 3.0 18.9 - - - +
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Residues in contact with ASP 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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98A VAL 3.6 0.8 - - - +
99A ILE* 3.3 6.9 - - - +
100A ARG* 2.5 50.6 + - + +
101A LYS 4.6 1.2 - - - +
102A LYS* 3.9 6.6 - - - -
103A PRO* 3.9 8.0 - - - +
106A ARG* 2.4 49.7 + - - -
109A ALA* 3.1 5.2 - - - +
110A ARG* 2.9 25.1 + - + +
92B ASP 4.0 0.6 + - - -
93B GLN* 1.3 72.5 - - - +
95B VAL* 1.3 63.2 + - - +
96B GLU* 4.1 1.6 - - + +
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Residues in contact with VAL 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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97A ILE* 3.7 17.5 - - + -
98A VAL 3.5 3.4 - - - -
99A ILE* 4.5 2.9 - - + -
110A ARG 2.9 9.3 + - - +
111A ILE* 3.0 17.6 - - + +
112A SER* 2.8 27.5 + - - +
39B LEU* 5.6 0.2 - - + -
85B MSE 3.4 52.3 - - + +
88B LEU* 4.1 24.0 - - + -
89B ASN* 3.8 13.2 - - - +
93B GLN 4.2 0.2 - - - +
94B ASP* 1.3 77.5 - - - +
96B GLU* 1.3 58.7 + - - +
97B ILE* 4.4 1.8 - - + -
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Residues in contact with GLU 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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96A GLU 3.3 3.5 - - - +
97A ILE* 3.5 1.0 - - - -
98A VAL* 2.7 51.2 + - + +
100A ARG* 2.7 40.8 + - - +
112A SER* 3.6 11.7 - - - +
114A VAL* 3.4 36.1 - - + +
94B ASP* 4.1 1.8 - - + -
95B VAL* 1.3 72.7 - - - +
97B ILE* 1.3 62.6 + - - +
98B VAL* 3.6 22.3 + - + +
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Residues in contact with ILE 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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35A THR* 3.9 18.6 - - + -
39A LEU* 4.1 24.2 - - + -
81A VAL* 5.0 0.4 - - + -
85A MSE 4.5 6.7 - - - -
95A VAL* 3.6 29.8 - - + -
96A GLU 3.6 2.5 - - - +
97A ILE* 4.5 4.7 - - + +
111A ILE* 3.8 20.4 - - + -
112A SER 2.8 14.3 + - - +
113A VAL* 3.4 12.7 - - + +
114A VAL 2.8 28.2 + - - +
85B MSE 3.7 31.6 - - + -
95B VAL* 4.4 1.6 - - + -
96B GLU* 1.3 72.0 - - - +
98B VAL* 1.3 59.0 + - - +
99B ILE* 3.8 4.7 + - + -
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Residues in contact with VAL 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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94A ASP 3.6 1.0 - - - +
95A VAL* 3.3 3.8 - - - -
96A GLU* 2.7 49.6 + - + +
98A VAL* 4.1 10.5 - - + -
114A VAL* 3.4 11.4 - - + +
116A ALA* 3.5 31.0 - - + -
96B GLU* 3.7 35.2 - - + +
97B ILE* 1.3 70.5 - - - +
99B ILE* 1.3 62.4 + - - +
100B ARG* 3.7 27.1 + - + +
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Residues in contact with ILE 99 (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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39A LEU* 4.1 2.9 - - + -
42A ALA* 3.6 29.6 - - + -
46A VAL* 5.8 1.6 - - + -
88A LEU* 3.9 27.6 - - + -
93A GLN* 3.9 30.5 - - + +
94A ASP 3.3 4.5 - - - +
95A VAL* 4.6 7.0 - - + -
113A VAL* 3.6 25.6 - - + -
114A VAL 2.8 15.9 + - - +
115A ALA* 3.5 7.2 - - + +
116A ALA 2.9 29.5 + - - +
97B ILE* 4.3 8.7 - - + +
98B VAL* 1.3 74.5 - - - +
100B ARG* 1.3 58.7 + - - +
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Residues in contact with ARG 100 (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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93A GLN* 3.2 7.8 - - - -
94A ASP* 2.7 51.6 + - + +
96A GLU* 2.7 45.7 + - - +
116A ALA* 3.6 32.1 - - + +
98B VAL* 3.7 16.7 + - + +
99B ILE* 1.3 76.3 - - - +
101B LYS* 1.3 66.8 + - - +
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Residues in contact with LYS 101 (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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46A VAL* 5.1 4.8 - - - +
91A LEU 4.2 3.6 + - - -
92A ASP* 3.3 27.6 - - + +
93A GLN* 2.8 28.5 + - - +
94A ASP* 4.5 0.5 - - - +
116A ALA 4.4 4.4 + - - -
100B ARG* 1.3 80.4 - - - +
102B LYS* 1.3 75.6 + - + +
103B PRO* 3.8 1.2 - - - +
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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