Contacts of the strand formed by residues 96 - 103 (chain A) in PDB entry 2O6F
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 ARG 96 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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94A TYR 4.5 4.5 - - - +
95A LEU* 1.3 76.7 - - - +
97A VAL* 1.3 61.1 + - - +
98A VAL* 4.1 8.0 + - + +
143A GLU 3.6 3.5 - - - +
145A ALA* 2.8 55.9 + - + +
146A ALA* 2.8 28.8 + - - +
147A PRO 3.8 8.3 + - - -
148A SER* 3.6 30.2 + - - +
303A CL 4.0 15.8 - - - +
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Residues in contact with VAL 97 (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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73A ALA* 4.5 11.2 - - + -
75A ILE* 3.7 18.4 - - + -
95A LEU* 3.9 3.9 + - + -
96A ARG* 1.3 75.0 - - - +
98A VAL* 1.3 72.3 + - - +
113A MET* 4.1 0.9 - - - +
114A PHE* 2.9 59.6 + - + +
125A TYR* 3.6 32.3 - - + -
142A PHE* 4.7 6.3 - - + -
143A GLU 3.5 7.9 - - - +
144A ILE* 4.2 18.8 - - + -
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Residues in contact with VAL 98 (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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96A ARG* 4.7 7.9 - - + +
97A VAL* 1.3 84.1 - - - +
99A ALA* 1.3 62.1 + - - +
100A PHE* 3.7 21.2 - - + -
111A LYS* 3.6 37.7 - - + -
112A VAL 3.4 12.1 - - - +
113A MET* 4.4 14.8 - - + -
141A ARG 3.7 0.3 - - - +
142A PHE* 3.4 2.4 - - - -
143A GLU* 2.8 38.6 + - + +
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Residues in contact with ALA 99 (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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71A ILE* 5.9 0.9 - - + -
98A VAL* 1.3 74.3 - - - +
100A PHE* 1.3 63.0 + - - +
101A LEU* 4.2 13.5 - - + -
110A GLN 3.6 0.7 - - - +
111A LYS* 3.6 2.6 - - - -
112A VAL* 2.7 40.2 + - + +
114A PHE* 3.5 34.8 - - + -
141A ARG 3.2 4.5 - - - +
142A PHE* 3.8 17.0 - - + -
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Residues in contact with PHE 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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98A VAL* 3.7 24.0 - - + -
99A ALA* 1.3 75.9 - - - +
101A LEU* 1.3 63.3 + - - +
109A VAL* 3.8 25.4 - - + -
110A GLN 3.2 8.5 - - - -
111A LYS* 3.6 28.5 - - + -
139A LYS 3.7 1.4 - - - +
140A VAL* 3.6 4.0 - - - -
141A ARG* 2.7 44.7 + - + +
143A GLU* 3.5 47.8 - - + -
302A CL 4.2 12.3 - - + -
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Residues in contact with LEU 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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71A ILE* 4.6 10.5 - - + -
99A ALA* 4.5 10.3 - - + -
100A PHE* 1.3 82.3 - - - +
102A GLN* 1.3 63.1 + - - +
103A LYS 4.3 0.2 - - - -
108A LYS 4.0 0.5 - - - +
109A VAL* 3.5 2.4 - - - -
110A GLN* 2.9 60.9 + - + +
112A VAL* 4.3 9.2 - - + -
129A VAL* 3.7 30.3 - - + -
131A PHE* 4.0 16.4 - - + -
138A TYR* 4.2 14.3 - - + -
139A LYS 3.4 3.4 - - - -
140A VAL* 3.9 30.3 - - + -
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Residues in contact with GLN 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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101A LEU* 1.3 76.3 - - - +
103A LYS* 1.3 66.4 + - - +
104A HIS* 3.5 1.0 + - - -
106A SER 2.9 25.9 + - - +
107A GLU* 4.0 10.5 + - - +
108A LYS 3.4 16.6 - - - +
109A VAL* 3.7 19.0 - - + +
138A TYR* 3.6 3.9 - - - -
139A LYS* 2.8 47.2 + - + +
302A CL 3.5 22.7 - - + +
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Residues in contact with LYS 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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102A GLN* 1.3 77.2 - - - +
104A HIS* 1.3 77.2 + - + +
105A GLY 3.3 0.3 + - - -
106A SER* 3.1 23.5 + - - +
108A LYS 4.4 4.0 + - - -
133A GLU* 2.7 54.3 + - + +
135A LEU 3.4 26.2 + - - +
136A GLY* 4.3 4.3 - - - -
137A THR 3.6 13.9 - - - +
138A TYR* 3.4 28.4 - - + +
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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