Contacts of the strand formed by residues 164 - 172 (chain B) 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 LEU 164 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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132B LEU* 4.0 40.8 - - + -
136B LEU* 3.9 27.6 - - + -
141B LEU* 4.2 10.5 - - + -
145B ALA 5.0 0.2 - - - +
147B ILE* 4.0 18.8 - - + -
160B THR* 3.4 9.2 - - - +
161B ILE* 2.8 37.2 + - + +
163B THR* 1.3 77.2 - - - +
165B LYS* 1.3 60.2 + - - +
180B TYR* 4.1 14.3 - - + -
181B ARG 3.5 3.8 - - - -
182B GLN* 3.7 34.3 - - + +
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Residues in contact with LYS 165 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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159B GLU 3.8 4.5 - - - +
160B THR* 4.7 12.6 - - + +
163B THR* 4.3 7.2 - - - +
164B LEU* 1.3 78.6 - - - +
166B LYS* 1.3 67.6 + - - +
167B THR* 3.3 9.0 + - + +
180B TYR* 3.3 3.7 - - - -
181B ARG 3.0 33.3 + - - +
183B GLU* 3.4 29.5 - - + +
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Residues in contact with LYS 166 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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157B LEU* 2.7 22.7 + - - +
158B PRO 3.4 19.7 - - - -
159B GLU* 2.9 46.6 + - - +
165B LYS* 1.3 72.2 - - - +
167B THR* 1.3 62.5 + - - +
168B ARG 3.8 6.7 - - - +
169B GLU* 2.7 45.3 + - + +
178B THR* 3.6 20.2 - - + -
179B ILE 3.4 12.6 - - - +
180B TYR* 3.5 10.1 - - + -
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Residues in contact with THR 167 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165B LYS* 3.5 18.8 - - + +
166B LYS* 1.3 75.9 - - - +
168B ARG* 1.3 97.8 + - - +
179B ILE* 2.9 17.4 + - - +
181B ARG* 3.9 22.7 - - + +
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Residues in contact with ARG 168 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35B MSE 3.2 46.3 + - + +
166B LYS* 3.8 6.4 - - - +
167B THR* 1.3 111.6 + - - +
169B GLU* 1.3 64.5 + - - +
170B THR* 5.2 1.3 - - - +
177B VAL 4.4 0.7 - - - -
178B THR* 3.5 0.7 - - - -
179B ILE* 2.8 51.6 + - + +
181B ARG* 2.7 48.8 - - - +
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Residues in contact with GLU 169 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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157B LEU* 4.3 6.0 + - - +
166B LYS* 2.7 39.1 + - + +
168B ARG* 1.3 77.4 - - - +
170B THR* 1.3 65.8 + - - +
171B VAL* 6.1 0.9 - - + -
176B GLN* 3.4 30.4 + - + +
177B VAL 3.2 5.8 - - - +
178B THR* 2.7 28.5 + - - +
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Residues in contact with THR 170 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35B MSE 4.5 13.5 - - - +
168B ARG* 5.2 0.9 - - - +
169B GLU* 1.3 80.4 + - - +
171B VAL* 1.3 74.9 + - - +
172B TYR* 3.7 37.2 + - + +
175B THR 3.9 0.5 - - - +
176B GLN* 3.7 1.7 - - - +
177B VAL* 2.8 36.2 + - - +
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Residues in contact with VAL 171 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153B LYS* 3.5 44.6 - - + +
169B GLU* 6.0 0.7 - - + -
170B THR* 1.3 84.8 - - - +
172B TYR* 1.3 72.0 + - - +
173B GLY 3.4 25.4 + - - +
174B ILE 4.7 2.0 - - - +
175B THR 3.5 10.3 - - - +
176B GLN* 4.3 13.2 - - + +
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Residues in contact with TYR 172 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27B LYS 6.2 0.4 - - - -
28B VAL* 3.8 26.9 - - + +
31B SER* 3.6 35.9 + - - -
32B ILE 5.4 0.2 - - - -
35B MSE 3.9 24.4 - - + +
170B THR* 3.7 33.1 + - + +
171B VAL* 1.3 76.1 - - - +
173B GLY* 1.3 54.2 + - - +
174B ILE* 2.7 17.7 + - - +
175B THR* 2.8 28.3 + - + +
177B VAL* 4.0 23.1 - - + -
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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