Contacts of the strand formed by residues 147 - 151 (chain A) in PDB entry 1OHT
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 TYR 147 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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36A ALA 4.2 3.8 - - - +
37A PRO 3.6 13.9 - - - +
39A VAL* 3.6 24.5 - - + -
134A ILE* 3.3 25.6 - - + +
138A VAL* 3.8 18.6 - - + -
143A ILE* 3.5 20.4 - - + -
144A ASP* 2.8 27.1 + - - +
145A PRO 3.3 1.9 - - - -
146A ALA* 1.3 79.5 - - - +
148A LYS* 1.3 66.4 + - - +
149A LEU* 4.1 13.8 - - + +
173A PRO* 3.9 12.1 + - - +
174A HIS* 2.7 72.7 + + + +
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Residues in contact with LYS 148 (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 PRO 3.0 9.7 + - - +
38A TYR* 3.4 43.0 + - + +
39A VAL 3.0 23.6 + - - +
146A ALA* 4.3 9.3 + - - +
147A TYR* 1.3 79.9 - - - +
149A LEU* 1.3 59.7 + - - +
150A LEU* 5.1 2.5 - - + -
174A HIS 3.9 4.0 - - - +
176A THR* 3.9 29.6 - - + +
178A ILE* 6.0 4.0 - - + -
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Residues in contact with LEU 149 (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* 3.6 22.9 - - + -
41A ILE* 3.7 30.3 - - + -
134A ILE* 4.5 8.5 - - + -
147A TYR* 4.0 13.1 - - + +
148A LYS* 1.3 71.4 - - - +
150A LEU* 1.3 66.9 + - - +
169A ILE* 3.7 14.8 - - + +
172A TRP* 3.4 42.0 - - + -
173A PRO 3.9 6.3 - - - +
174A HIS 3.1 18.4 + - - +
175A PHE* 3.4 12.2 - - + -
176A THR 3.1 23.2 + - - -
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Residues in contact with LEU 150 (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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38A TYR* 3.9 23.8 - - + -
39A VAL 2.9 9.2 + - - +
40A ILE* 3.4 15.3 - - + -
41A ILE* 2.8 28.8 + - - +
104A TYR* 4.3 2.7 - - + -
148A LYS* 4.5 6.5 - - + +
149A LEU* 1.3 78.7 - - - +
151A GLY* 1.3 66.2 + - - +
154A GLN* 3.1 17.7 - - - +
155A VAL* 3.9 24.2 - - + -
169A ILE* 4.0 5.8 - - - -
175A PHE* 4.7 1.1 - - - -
176A THR* 3.4 32.1 - - - +
178A ILE* 3.9 26.0 - - + -
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Residues in contact with GLY 151 (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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40A ILE* 4.1 2.8 - - - +
41A ILE 3.6 7.9 - - - -
150A LEU* 1.3 78.4 - - - +
152A HIS* 1.3 67.3 + - - +
153A ARG* 3.2 3.6 - - - -
154A GLN* 2.7 29.7 + - - +
155A VAL* 4.2 2.4 + - - +
161A PRO* 3.9 8.3 - - - -
166A PHE* 4.1 4.7 - - - -
169A ILE* 3.7 17.8 - - - +
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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