Contacts of the strand formed by residues 88 - 93 (chain A) in PDB entry 1OJ7
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 PHE 88 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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25A GLN 5.0 1.3 - - - -
26A ILE* 3.9 29.4 - - + -
27A PRO* 4.2 22.9 - - + -
30A ALA* 4.0 17.9 - - + -
31A ARG 3.3 4.0 + - - +
32A VAL* 3.3 11.2 - - + -
33A LEU 3.0 24.6 + - - -
86A VAL* 3.4 4.7 - - - +
87A THR* 1.3 79.3 - - - +
89A LEU* 1.3 90.3 + - - +
90A LEU* 4.5 2.0 - - - -
131A ILE* 3.7 1.1 - - - +
132A PRO* 3.6 35.4 - - + -
133A MET 3.8 3.1 - - - -
134A GLY* 3.7 14.4 - - - -
171A VAL* 4.6 8.1 - - + -
172A PHE* 3.6 24.9 - + - -
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Residues in contact with LEU 89 (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 LEU* 3.5 38.1 - - + +
35A THR* 4.4 2.9 - - + -
81A VAL* 4.3 5.6 - - + -
86A VAL* 4.3 2.2 - - + -
88A PHE* 1.3 80.3 - - - +
90A LEU* 1.3 59.9 + - - +
91A ALA 4.1 0.4 - - - -
101A THR* 3.7 24.7 - - + +
104A ILE* 4.1 14.8 - - + -
105A ALA* 3.6 42.8 - - + +
131A ILE* 3.9 20.2 - - + +
132A PRO 3.0 7.1 + - - -
133A MET* 3.1 11.1 - - + +
134A GLY 3.0 24.6 + - - -
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Residues in contact with LEU 90 (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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22A LEU* 4.1 15.7 - - + -
26A ILE* 4.3 3.1 - - + -
32A VAL* 4.1 14.8 - - + +
33A LEU 3.0 10.4 + - - +
34A ILE* 3.3 9.2 - - + +
35A THR* 2.9 26.3 + - - +
50A VAL* 3.7 30.3 - - + -
54A LEU* 3.8 19.3 - - + -
88A PHE* 4.3 3.1 + - + -
89A LEU* 1.3 72.9 - - - +
91A ALA* 1.3 59.7 + - - +
92A VAL* 3.7 7.7 + - + -
134A GLY 3.6 22.0 - - - +
135A CYS* 3.8 11.7 - - - +
136A VAL* 4.3 2.5 - - + -
172A PHE* 3.9 22.7 - - + -
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Residues in contact with ALA 91 (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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35A THR* 3.2 8.3 - - - +
89A LEU 4.1 1.2 - - - -
90A LEU* 1.3 71.0 - - - +
92A VAL* 1.3 55.1 + - - +
93A GLY 4.0 0.7 - - - -
97A VAL* 4.0 2.2 - - + -
98A LEU* 3.9 23.3 - - + +
101A THR* 3.5 28.7 - - - +
133A MET* 3.9 7.9 - - + -
134A GLY 3.0 14.3 + - - +
135A CYS* 3.1 4.1 - - + +
136A VAL* 2.8 32.2 + - - +
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Residues in contact with VAL 92 (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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34A ILE* 3.8 26.9 - - + -
35A THR 2.9 10.9 + - - +
36A TYR* 3.4 27.2 - - + +
37A GLY 4.3 0.3 + - - -
41A VAL* 3.9 16.8 - - + +
46A VAL* 4.0 26.7 - - + -
47A LEU* 5.1 5.2 - - + -
50A VAL* 4.1 20.4 - - + -
90A LEU* 3.9 12.3 - - + +
91A ALA* 1.3 77.2 - - - +
93A GLY* 1.3 58.0 + - - +
97A VAL* 3.8 3.7 - - - +
136A VAL* 3.4 15.9 - - + +
138A THR* 4.6 0.9 - - + -
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Residues in contact with GLY 93 (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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37A GLY 5.6 0.4 - - - -
41A VAL* 4.7 3.8 - - - -
91A ALA 4.0 1.6 - - - -
92A VAL* 1.3 75.3 - - - +
94A GLY* 1.3 64.2 + - - +
97A VAL* 4.1 10.2 - - - +
98A LEU* 3.7 2.8 - - - +
136A VAL 3.1 7.7 + - - +
137A LEU* 3.5 10.7 - - - +
138A THR* 2.9 38.8 + - - +
1388A NZQ 5.3 3.4 - - - -
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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