Contacts of the strand formed by residues 99 - 104 (chain A) in PDB entry 2OB1
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 99 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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92A PHE* 4.0 4.9 - - + -
93A LEU* 3.7 26.7 - - + -
96A ASN* 2.8 50.3 - - + +
97A GLU 3.7 2.1 + - - +
98A LYS* 1.3 75.7 - - - +
100A GLN* 1.3 83.2 + - - +
121A HIS 3.5 6.3 + - - +
122A LEU* 3.4 6.6 - - + -
123A ALA* 2.9 24.3 + - - +
194A ILE* 3.7 5.7 - - - +
195A PRO* 3.2 22.2 - - + +
197A ILE* 4.1 12.1 - - + -
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Residues in contact with GLN 100 (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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99A VAL* 1.3 80.0 - - - +
101A VAL* 1.3 63.3 + - - +
102A VAL* 4.1 0.4 - - + -
123A ALA* 3.1 18.6 - - + +
125A VAL* 5.9 2.0 - - + -
189A CYS 4.7 1.4 - - - +
190A THR* 3.5 21.8 - - + -
191A LYS* 2.7 42.4 + - - +
194A ILE* 3.2 23.3 + - + +
195A PRO 2.9 6.5 + - - +
196A THR* 2.6 38.7 + - + +
197A ILE 2.8 25.1 + - - +
223A PHE* 3.4 11.3 - - - -
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Residues in contact with VAL 101 (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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89A ILE* 5.1 4.0 - - + -
93A LEU* 4.3 4.9 - - + -
100A GLN* 1.3 74.9 - - - +
102A VAL* 1.3 65.9 + - - +
115A LEU* 5.5 0.9 - - + -
122A LEU* 3.5 22.4 - - + -
123A ALA 2.8 7.1 + - - +
124A TYR* 3.5 37.6 - - + -
125A VAL* 2.8 33.4 + - - +
197A ILE* 3.3 34.8 - - + +
199A ILE* 3.6 25.1 - - + -
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Residues in contact with VAL 102 (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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100A GLN 5.1 0.7 - - - -
101A VAL* 1.3 78.6 - - - +
103A ASN* 1.3 60.9 + - - +
104A LEU* 3.5 27.5 + - + -
125A VAL* 3.5 7.2 - - + +
127A ILE* 3.9 20.2 - - + -
186A LEU* 3.9 12.8 - - + -
190A THR* 4.0 26.7 - - + -
196A THR* 4.0 18.8 - - + -
197A ILE 2.7 11.0 + - - +
198A VAL* 3.4 10.4 - - + +
199A ILE 2.8 26.6 + - - +
219A ILE* 5.8 1.8 - - + -
223A PHE* 4.9 4.0 - - + -
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Residues in contact with ASN 103 (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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101A VAL 4.0 1.0 - - - -
102A VAL* 1.3 70.7 - - - +
104A LEU* 1.3 66.3 + - - +
105A GLY 4.3 0.5 - - - +
106A CYS* 3.6 18.5 - - - +
109A ASP* 2.9 29.3 + - - +
124A TYR* 2.9 28.4 + - + +
125A VAL 2.8 11.0 + - - +
126A ASP* 3.5 18.2 + - - +
127A ILE* 3.0 28.6 + - - +
199A ILE* 3.8 26.8 - - + +
201A GLU* 5.3 2.8 + - - +
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Residues in contact with LEU 104 (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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102A VAL* 3.7 21.8 - - + -
103A ASN* 1.3 75.0 - - - +
105A GLY* 1.3 65.1 + - - +
127A ILE* 3.9 9.2 - - + -
176A LEU* 3.8 22.2 - - + -
182A THR* 5.1 1.6 - - + -
186A LEU* 5.7 0.4 - - + -
198A VAL* 3.5 28.5 - - + -
199A ILE 2.9 20.8 + - - +
200A SER* 4.0 3.3 - - - -
201A GLU 4.5 1.6 + - - -
203A LEU* 3.5 29.1 - - + +
215A LEU* 4.2 10.8 - - + -
219A ILE* 3.9 22.9 - - + -
228A TRP* 3.8 17.3 - - + -
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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