Contacts of the strand formed by residues 172 - 176 (chain B) in PDB entry 1HCS
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 172 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148B TRP* 3.6 24.9 - + + -
162B LEU* 4.1 1.3 - - - -
170B GLY 3.7 4.5 - - - -
171B THR* 1.3 74.8 - - - +
173B LEU* 1.3 65.6 + - - +
186B LEU* 3.4 17.9 - - + -
187B SER 2.9 21.3 - - - +
188B VAL* 3.9 4.0 - - + +
227B VAL* 3.9 20.6 - - + -
231B SER* 4.6 2.0 - - - -
241B LEU* 3.6 48.0 - - + -
242B THR 4.8 0.4 - - - -
243B THR 2.6 36.9 + - - -
244B VAL* 3.4 21.7 - - + -
245B CYS* 2.9 27.6 + - - +
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Residues in contact with LEU 173 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148B TRP 4.5 3.1 - - - +
150B PHE* 5.6 8.7 - - + +
153B ILE* 4.5 9.9 - - + -
158B SER* 4.4 11.7 - - - +
161B LEU* 4.7 5.4 - - + -
162B LEU* 3.6 26.0 - - + -
172B PHE* 1.3 83.6 - - - +
174B VAL* 1.3 72.1 + - - +
175B ARG* 4.2 25.6 - - + +
185B CYS 3.4 1.0 - - - +
186B LEU* 4.0 0.9 - - - -
187B SER* 3.1 26.9 + - - +
244B VAL* 4.8 3.6 - - - -
245B CYS* 3.2 38.4 - - + +
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Residues in contact with VAL 174 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148B TRP* 3.0 62.9 + - + +
149B TYR* 3.5 6.7 - - + -
150B PHE 3.4 15.9 + - - -
172B PHE* 4.5 0.2 - - + -
173B LEU* 1.3 74.5 - - - +
175B ARG* 1.3 61.8 + - - +
184B TYR* 4.2 17.3 - - + -
185B CYS 3.5 4.3 - - - +
186B LEU* 3.4 21.1 - - + -
204B ILE* 3.7 27.8 - - + -
223B LEU* 4.6 2.2 - - + -
227B VAL* 4.2 9.0 - - + -
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Residues in contact with ARG 175 (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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101A PTR 3.1 37.9 + - - -
149B TYR* 4.6 2.9 - - - -
150B PHE* 5.3 1.8 - - + -
151B GLY 3.1 19.7 - - - +
153B ILE* 3.6 28.8 + - + +
154B THR 4.2 2.0 + - - -
155B ARG* 4.0 15.8 - - - +
158B SER* 3.0 37.7 + - - -
173B LEU* 4.2 8.4 - - + +
174B VAL* 1.3 75.5 - - - +
176B GLU* 1.3 72.2 + - - +
178B GLU* 5.3 5.7 - - - +
184B TYR* 3.5 15.0 - - - +
185B CYS* 3.2 49.0 + - + +
187B SER* 4.2 13.8 + - - -
201B HIS* 4.6 4.6 + - - -
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Residues in contact with GLU 176 (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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149B TYR* 3.6 20.5 + - - +
151B GLY* 3.0 14.5 + - - +
152B LYS* 4.2 28.4 + - + +
175B ARG* 1.3 95.0 - - - +
177B SER* 1.3 71.7 + - - +
178B GLU* 3.0 6.8 + - - +
183B ALA 4.2 6.7 - - - +
184B TYR* 4.4 10.3 - - + +
185B CYS* 4.3 2.0 - - - -
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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