Contacts of the strand formed by residues 175 - 181 (chain A) in PDB entry 2FHP
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 THR 175 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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22A ARG* 2.8 33.1 + - - +
23A PRO* 3.4 12.5 + - - +
28A VAL* 4.3 22.0 - - + +
150A GLU* 3.7 21.8 - - + +
151A THR 3.7 2.5 - - - -
170A THR 3.8 0.9 - - - +
171A VAL* 3.5 2.3 - - - -
172A TYR* 2.8 40.4 + - - +
173A GLY 3.4 0.2 - - - -
174A ILE* 1.3 78.8 - - - +
176A GLN* 1.3 70.3 + - - +
177A VAL* 3.9 3.0 + - + -
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Residues in contact with GLN 176 (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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149A CYS 3.5 1.0 - - - +
150A GLU* 3.3 6.4 - - - -
151A THR* 2.8 54.8 + - - +
152A ASP 3.4 5.7 - - - +
153A LYS* 4.0 20.6 + - - +
155A VAL* 2.9 27.3 + - - +
157A LEU* 5.3 1.5 - - - +
169A GLU* 3.2 37.7 + - + +
170A THR 3.6 6.5 - - - +
171A VAL* 4.3 13.7 - - + +
174A ILE 3.8 0.6 + - - -
175A THR* 1.3 73.5 - - - +
177A VAL* 1.3 61.9 + - - +
178A THR* 3.9 10.7 + - - +
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Residues in contact with VAL 177 (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* 3.9 20.9 - - + -
32A ILE* 3.8 25.8 - - + -
35A MSE 4.1 11.4 - - + +
148A VAL* 4.2 3.1 - - + -
149A CYS 3.3 8.3 - - - +
150A GLU* 4.7 2.2 - - + -
168A ARG 4.1 0.5 - - - +
169A GLU* 3.2 4.9 - - - +
170A THR 2.8 37.7 + - - +
172A TYR* 3.8 28.3 - - + -
175A THR* 4.4 4.9 - - + -
176A GLN* 1.3 75.0 - - - +
178A THR* 1.3 63.2 + - - +
179A ILE* 4.0 21.8 - - + +
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Residues in contact with THR 178 (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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147A ILE 3.6 2.1 - - - +
148A VAL* 3.6 1.6 - - - -
149A CYS* 2.8 41.6 + - - +
151A THR* 4.8 0.2 + - - -
157A LEU* 3.6 21.8 - - + +
166A LYS* 3.6 28.9 - - + -
168A ARG 3.6 2.5 - - - -
169A GLU* 2.7 30.7 + - - +
176A GLN* 3.9 8.0 + - - +
177A VAL* 1.3 74.9 - - - +
179A ILE* 1.3 66.2 + - - +
180A TYR* 3.7 16.8 - - + -
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Residues in contact with ILE 179 (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 ILE* 5.5 0.9 - - + -
35A MSE 4.5 13.0 - - + -
36A ILE* 4.0 10.5 - - + -
146A VAL* 3.5 26.9 - - + -
147A ILE 3.3 0.9 - - - -
148A VAL* 3.8 25.4 - - + -
166A LYS* 3.4 7.1 - - - +
167A THR* 2.8 42.2 + - - +
168A ARG* 2.8 50.6 + - + +
177A VAL* 4.0 17.0 - - + +
178A THR* 1.3 82.1 - - - +
180A TYR* 1.3 60.5 + - - +
181A ARG* 4.5 0.2 - - - +
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Residues in contact with TYR 180 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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128A ILE* 5.1 0.9 - - + -
132A LEU* 4.2 9.6 - - + -
146A VAL* 3.6 2.3 - - - +
147A ILE* 2.9 48.3 + - + +
149A CYS* 4.0 25.1 - - - -
157A LEU* 3.3 23.3 - - + +
158A PRO* 2.6 34.9 + - - +
159A GLU 4.2 2.7 - - - -
161A ILE* 3.5 24.3 - - + +
164A LEU* 4.2 19.7 - - + -
165A LYS* 3.3 7.2 - - - -
166A LYS* 3.4 29.8 - - + -
178A THR* 3.7 20.0 - - + -
179A ILE* 1.3 74.8 - - - +
181A ARG* 1.3 69.8 + - - +
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Residues in contact with ARG 181 (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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36A ILE* 4.2 17.6 + - - +
144A GLU* 4.2 13.7 + - - +
145A ALA 4.1 10.2 + - - +
146A VAL* 3.8 30.2 - - + +
164A LEU* 3.8 7.0 - - - -
165A LYS* 2.8 34.4 + - - +
167A THR* 3.9 19.0 - - + +
168A ARG* 2.8 45.1 - - - +
180A TYR* 1.3 79.6 - - - +
182A GLN* 1.3 67.4 + - - +
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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