Contacts of the strand formed by residues 120 - 125 (chain A) in PDB entry 2OHF
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 ILE 120 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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25A ILE* 4.2 5.4 - - - +
26A GLY* 3.6 2.7 - - - -
28A VAL* 3.6 28.9 - - + -
114A ILE* 4.2 26.7 - - + -
117A CYS* 6.1 0.7 - - + -
119A GLY* 1.3 75.5 - - - +
121A PHE* 1.3 63.5 + - - +
122A HIS* 3.2 23.1 + - + +
152A LEU* 4.5 9.0 - - + -
220A LEU 4.3 8.7 - - - +
223A LYS* 4.1 23.8 - - + +
224A PRO 2.6 14.3 + - - +
225A MET* 3.2 25.8 - - + -
226A VAL* 2.9 27.2 + - - +
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Residues in contact with PHE 121 (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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25A ILE* 3.6 35.6 - - + +
26A GLY 2.8 13.9 + - - +
27A ILE* 3.8 7.0 - - + -
28A VAL 3.0 17.5 + - - -
38A PHE* 3.8 30.5 - + + -
42A LEU* 5.1 2.2 - - + -
88A LEU* 4.3 8.1 - - + -
90A VAL* 4.3 18.4 - - + -
120A ILE* 1.3 69.6 - - - +
122A HIS* 1.3 60.3 + - - +
123A LEU* 2.8 11.0 + - - +
226A VAL* 3.5 13.7 - - + -
228A LEU* 4.0 21.8 - - + -
295A ILE* 3.4 40.6 - - + -
296A ILE* 5.0 0.4 - - - -
299A GLY* 3.9 16.2 - - - -
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Residues in contact with HIS 122 (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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28A VAL* 3.4 12.6 - - + -
29A GLY* 4.8 0.6 - - - -
120A ILE* 3.2 9.7 + - + +
121A PHE* 1.3 67.9 - - - +
123A LEU* 1.3 75.1 + - - +
124A THR* 3.9 9.8 + - - -
144A ASP 5.2 0.6 - - - -
145A ILE* 3.8 30.1 - - + +
148A ILE* 3.6 41.6 - - + +
149A HIS* 4.4 3.1 - + - -
225A MET* 3.0 38.8 - - + -
226A VAL 2.8 14.9 + - - +
227A TYR* 3.6 16.4 - + - +
228A LEU* 3.0 22.0 + - - +
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Residues in contact with LEU 123 (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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27A ILE* 4.5 6.5 - - + -
28A VAL 2.9 15.1 + - - +
29A GLY* 4.0 7.9 - - - -
33A VAL* 3.9 17.1 - - + +
34A GLY 3.7 8.7 - - - +
35A LYS* 3.6 41.3 - - + +
38A PHE* 4.1 14.1 - - + -
121A PHE 2.8 12.1 + - - +
122A HIS* 1.3 79.0 + - - +
124A THR* 1.3 79.5 + - - +
228A LEU* 3.4 13.2 - - + +
230A ASN* 4.1 7.6 - - + -
263A PHE* 3.3 38.1 - - + -
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Residues in contact with THR 124 (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 VAL* 4.9 5.1 - - - +
122A HIS* 3.9 17.0 + - - -
123A LEU* 1.3 85.0 + - - +
125A ARG* 1.3 60.6 + - - +
141A PRO* 3.7 31.4 + - + +
144A ASP* 5.5 6.3 - - + +
145A ILE* 4.1 14.9 - - + +
227A TYR* 5.5 1.9 - - - -
228A LEU 3.0 12.1 + - - +
229A VAL* 3.4 7.5 - - + -
230A ASN* 2.5 38.0 + - - +
247A ILE* 4.5 13.5 - - + -
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Residues in contact with ARG 125 (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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32A ASN* 3.6 27.2 + - - +
33A VAL* 4.1 28.4 - - + +
124A THR* 1.3 75.8 - - - +
126A ALA* 1.3 73.5 + - - +
140A ASP* 4.9 5.4 - - - +
141A PRO* 3.6 24.3 - - - +
144A ASP* 5.3 7.8 + - - +
230A ASN* 3.7 7.0 - - + +
9001A ACP 5.1 15.3 + - - +
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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