Contacts of the strand formed by residues 136 - 145 (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 GLY 136 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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103A LYS* 4.3 8.5 - - - -
134A GLY 3.6 1.8 + - - -
135A LEU* 1.3 75.2 - - - +
137A THR* 1.3 61.3 + - - -
138A TYR* 3.5 9.8 - - - -
179A GLU* 3.7 14.1 - - - -
180A TRP 2.8 33.8 + - - -
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Residues in contact with THR 137 (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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103A LYS* 3.6 7.9 - - - +
104A HIS* 2.8 61.4 + - + +
136A GLY* 1.3 71.0 - - - -
138A TYR* 1.3 62.1 + - - +
177A ASP* 3.8 21.5 - - + +
178A PHE 3.3 9.0 - - - +
179A GLU* 2.6 25.7 + - - +
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Residues in contact with TYR 138 (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* 4.2 6.3 - - + -
102A GLN* 3.4 13.7 - - - -
103A LYS* 3.4 35.9 - - + -
104A HIS* 4.0 5.4 - - - -
110A GLN* 4.6 11.7 - - - -
131A PHE* 3.7 33.5 - + + +
133A GLU* 3.1 28.6 + - + -
134A GLY 2.7 30.8 + - - -
136A GLY 3.5 19.7 - - - -
137A THR* 1.3 75.2 - - - +
139A LYS* 1.3 66.8 + - - +
140A VAL* 3.7 10.7 + - + -
176A ASP 3.7 1.6 - - - +
178A PHE* 2.8 41.7 + - + +
180A TRP* 4.1 6.5 - - + -
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Residues in contact with LYS 139 (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 PHE 3.7 1.5 - - - +
101A LEU* 3.4 4.7 - - - -
102A GLN* 2.8 47.0 + - + +
104A HIS* 3.9 6.6 - - + +
138A TYR* 1.3 73.9 - - - +
140A VAL* 1.3 66.2 + - - +
141A ARG* 4.2 4.5 - - - +
174A GLU* 3.0 30.2 + - - +
175A TRP 3.4 11.4 - - - +
176A ASP* 3.0 36.6 + - + +
302A CL 4.1 21.3 - - + -
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Residues in contact with VAL 140 (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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33A ILE* 4.3 14.6 - - + -
71A ILE* 5.5 2.5 - - + -
100A PHE 3.6 2.5 - - - -
101A LEU* 3.9 24.9 - - + -
131A PHE* 5.1 2.7 - - + -
138A TYR* 4.3 5.4 - - + +
139A LYS* 1.3 78.5 - - - +
141A ARG* 1.3 62.5 + - - +
142A PHE* 3.8 27.1 - - + -
174A GLU* 3.2 3.5 - - - +
175A TRP* 2.8 54.2 + - + +
178A PHE* 3.8 35.0 - - + -
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Residues in contact with ARG 141 (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 0.5 - - - +
99A ALA* 3.2 4.0 - - - -
100A PHE* 2.7 51.7 + - + +
139A LYS* 4.2 4.6 - - - +
140A VAL* 1.3 76.2 - - - +
142A PHE* 1.3 64.5 + - - +
143A GLU* 2.7 38.4 + - + +
172A VAL* 3.5 29.8 - - + +
173A ALA 3.6 3.8 - - - -
174A GLU* 3.2 37.1 + - - +
302A CL 4.4 18.2 - - + -
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Residues in contact with PHE 142 (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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33A ILE* 3.9 7.6 - - + -
44A VAL* 4.1 9.9 - - + -
45A GLY 4.1 5.6 - - - -
46A GLY* 4.1 1.8 - - - -
71A ILE* 3.9 22.4 - - + -
73A ALA* 3.5 32.5 - - + -
97A VAL* 4.7 4.5 - - + -
98A VAL 3.4 4.5 - - - +
99A ALA* 3.8 10.8 - - + -
114A PHE* 3.8 22.7 - + - -
140A VAL* 3.8 18.8 - - + -
141A ARG* 1.3 81.8 - - - +
143A GLU* 1.3 61.8 + - - +
144A ILE* 4.1 11.5 + - + +
171A LEU 3.6 1.0 - - - +
172A VAL* 3.3 6.6 - - - +
173A ALA* 2.7 38.2 + - + +
175A TRP* 3.6 32.5 - + - -
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Residues in contact with GLU 143 (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 3.6 2.1 - - - +
97A VAL* 3.5 3.1 - - - +
98A VAL* 2.8 39.0 + - + +
100A PHE* 3.5 31.7 - - + -
141A ARG* 2.7 42.1 + - + +
142A PHE* 1.3 77.0 - - - +
144A ILE* 1.3 59.9 + - - +
145A ALA 4.0 0.4 - - - -
170A PRO* 4.4 18.1 - - + +
171A LEU 3.4 4.5 - - - +
172A VAL* 4.3 7.9 - - + -
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Residues in contact with ILE 144 (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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39A VAL* 4.8 6.5 - - + -
42A LEU* 3.7 24.9 - - + -
44A VAL* 3.7 36.1 - - + -
75A ILE* 4.0 15.9 - - + -
95A LEU* 3.8 19.5 - - + -
96A ARG 3.7 2.7 - - - -
97A VAL* 4.2 18.2 - - + +
142A PHE* 4.5 11.2 - - + +
143A GLU* 1.3 76.2 - - - +
145A ALA* 1.3 63.2 + - - +
167A TRP* 2.9 20.9 + - + -
170A PRO* 4.0 2.2 - - - +
171A LEU* 2.7 33.8 + - + +
173A ALA* 4.9 2.5 - - + -
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Residues in contact with ALA 145 (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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95A LEU* 3.4 9.4 - - - +
96A ARG* 2.8 58.3 + - + +
143A GLU 4.0 0.6 - - - -
144A ILE* 1.3 76.4 - - - +
146A ALA* 1.3 66.7 + - - +
167A TRP* 3.7 3.4 - - - +
168A SER 6.1 1.3 - - - +
170A PRO* 4.3 19.3 - - + -
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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