Contacts of the strand formed by residues 95 - 102 (chain A) in PDB entry 2OM5
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 ALA 95 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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13A PRO* 3.4 37.0 - - + +
14A LEU 3.5 20.2 - - - +
15A SER* 3.9 4.9 - - - +
29A LEU* 4.6 8.7 - - + -
78A VAL* 3.7 2.4 - - - -
79A TYR* 3.0 36.9 + - + +
93A ARG 3.7 0.6 + - - -
94A GLU* 1.3 72.6 - - - +
96A ILE* 1.3 63.6 + - - +
97A LEU 3.8 1.2 + - - -
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Residues in contact with ILE 96 (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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15A SER* 3.3 18.6 + - - +
16A VAL 2.9 29.3 + - - +
29A LEU* 6.4 0.7 - - - -
77A GLY 3.6 7.4 - - - +
78A VAL* 4.4 20.2 - - + -
94A GLU* 5.6 3.4 - - + +
95A ALA* 1.3 74.7 - - - +
97A LEU* 1.3 60.9 + - - +
98A ARG* 3.6 34.4 + - + +
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Residues in contact with LEU 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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16A VAL* 3.5 26.7 - - + +
18A PHE* 4.2 17.0 - - + -
27A VAL* 4.4 15.0 - - + -
29A LEU* 5.2 8.5 - - + -
67A ILE* 3.9 18.2 - - + -
75A ASP* 3.4 27.6 - - + +
76A ALA* 3.4 7.4 - - - +
77A GLY 2.9 26.7 + - - +
79A TYR* 3.6 28.5 - - + +
95A ALA 3.8 1.4 + - - -
96A ILE* 1.3 70.9 - - - +
98A ARG* 1.3 67.3 + - - +
99A PHE* 4.0 13.9 - - + -
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Residues in contact with ARG 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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16A VAL 2.9 9.0 + - - +
17A LEU* 3.4 18.0 - - + -
18A PHE* 2.9 28.6 + - - +
72A LYS* 5.5 7.4 - - - +
76A ALA* 4.8 16.2 - - - +
77A GLY* 4.8 8.9 - - - +
96A ILE* 3.6 26.7 + - + +
97A LEU* 1.3 81.0 + - - +
99A PHE* 1.3 68.3 + - - +
131A TYR* 4.0 32.8 + - + +
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Residues in contact with PHE 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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17A LEU* 3.9 2.9 - - - -
18A PHE* 3.2 38.6 - + + +
20A GLU* 4.5 16.6 - - + +
70A PRO* 3.7 29.4 - - + -
71A THR* 3.6 18.4 - - - -
72A LYS* 3.6 35.8 - - + +
75A ASP* 4.0 4.9 - - + -
76A ALA* 3.6 32.5 - - + -
97A LEU* 4.0 17.3 - - + -
98A ARG* 1.3 78.9 - - - +
100A GLY* 1.3 60.2 + - - +
101A PHE* 3.5 18.0 - - + -
131A TYR* 3.7 13.0 - - - +
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Residues in contact with GLY 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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17A LEU* 3.7 7.9 - - - +
18A PHE 2.9 12.7 + - - -
19A PRO* 3.4 5.7 - - - +
20A GLU* 2.8 27.9 + - - +
99A PHE* 1.3 69.1 - - - +
101A PHE* 1.3 61.1 + - - -
131A TYR 3.2 12.8 - - - -
183A MET* 3.8 25.8 - - - +
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Residues in contact with PHE 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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20A GLU* 3.5 36.1 - - + +
21A GLU* 6.1 0.7 - - - -
72A LYS* 4.8 23.3 - - + -
99A PHE* 3.5 15.0 - - + -
100A GLY* 1.3 74.0 - - - +
102A LEU* 1.3 63.3 + - - +
103A GLN* 4.5 14.4 - - + +
129A ALA* 3.4 22.9 - - + -
130A HIS* 3.2 34.0 - - - +
131A TYR* 2.9 46.7 + - + +
134A LEU* 5.6 0.2 - - - +
181A SER* 5.2 2.5 + - - -
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Residues in contact with LEU 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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21A GLU* 6.0 0.2 + - - -
101A PHE* 1.3 77.0 - - - +
103A GLN* 1.3 79.3 + - - +
128A PRO* 4.0 8.7 - - + -
129A ALA 3.7 2.9 - - - -
130A HIS* 4.0 18.8 - - + -
134A LEU* 4.3 13.0 - - + -
179A ALA 4.5 1.6 - - - +
181A SER* 4.1 19.5 - - - +
188A LYS* 3.2 69.6 + - + +
190A VAL* 3.8 24.7 - - + +
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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