Contacts of the strand formed by residues 171 - 177 (chain B) in PDB entry 6S1M
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 171 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82B LEU* 5.4 0.9 - - + -
85B LEU* 4.1 14.6 - - + -
91B CYS* 4.9 2.0 - - - -
93B VAL* 3.7 31.6 - - + -
135B LEU* 6.3 1.3 - - + -
142B ILE* 4.2 17.0 - - + -
143B LYS 3.4 18.3 + - - +
144B LEU* 3.7 12.8 - - + -
145B LYS* 3.0 30.2 + - - +
161B VAL* 4.4 8.5 - - + -
162B PHE 4.4 1.3 - - - -
163B GLY* 3.8 27.1 - - - -
164B SER* 3.7 14.1 - - - -
165B VAL* 4.1 12.6 - - + -
166B ARG* 5.7 0.9 - - - -
170B LYS* 1.3 77.3 - - - +
172B LEU* 1.3 75.9 + - - +
173B VAL* 3.8 19.7 - - + +
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Residues in contact with LEU 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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88B GLU* 6.1 0.7 - - - +
90B LYS* 5.2 6.0 + - - +
145B LYS* 3.5 19.1 - - + +
146B GLY* 4.3 11.9 - - - -
163B GLY* 3.3 24.8 - - - -
164B SER* 3.2 17.8 + - - +
166B ARG* 4.5 30.9 - - + +
171B PHE* 1.3 74.6 - - - +
173B VAL* 1.3 65.0 + - - +
174B GLU* 5.0 14.6 - - + +
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Residues in contact with VAL 173 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144B LEU* 4.2 20.4 - - + -
145B LYS 3.2 16.5 + - - +
146B GLY* 4.2 1.4 - - - -
147B THR* 3.0 42.1 + - - +
148B ILE* 4.4 9.9 - - + -
161B VAL* 3.7 33.7 - - + -
162B PHE 3.6 2.9 - - - -
171B PHE* 3.8 15.7 - - + -
172B LEU* 1.3 80.0 - - - +
174B GLU* 1.3 63.2 + - - +
175B ASP 4.1 7.9 - - - +
176B TYR* 4.3 10.5 - - + -
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Residues in contact with GLU 174 (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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90B LYS* 2.5 38.3 + - - +
147B THR* 3.1 19.7 + - - +
162B PHE* 3.0 42.0 + - - +
163B GLY* 4.5 1.6 - - - -
172B LEU* 5.0 9.8 - - + +
173B VAL* 1.3 77.2 - - - +
175B ASP* 1.3 69.1 + - - +
176B TYR* 5.8 0.2 - - - -
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Residues in contact with ASP 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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73B TRP* 2.3 33.6 + - - -
161B VAL* 4.1 0.3 - - - +
162B PHE* 3.0 51.4 + - - +
173B VAL* 3.9 1.8 - - - -
174B GLU* 1.3 82.0 - - - +
176B TYR* 1.3 70.1 + - - +
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Residues in contact with TYR 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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72B HIS* 5.5 2.6 - - - -
73B TRP* 3.8 4.9 - - - -
147B THR 3.9 13.7 - - - -
148B ILE* 3.6 32.9 - - + -
149B ASP* 4.1 19.6 + - - +
153B LEU* 4.6 8.2 - - + +
159B LEU* 4.0 21.8 - - + -
160B ALA 3.3 15.0 - - - +
161B VAL* 3.8 12.1 - - + -
173B VAL* 4.3 2.9 - - + -
175B ASP* 1.3 85.2 - - - +
177B CYS* 1.3 63.7 + - - +
178B PHE* 4.3 24.7 - + - -
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Residues in contact with CYS 177 (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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65B LEU* 3.6 6.3 - - - +
68B ARG* 4.6 6.1 - - - -
69B ALA* 4.4 20.4 - - - -
72B HIS* 3.7 30.1 - - + +
73B TRP* 4.1 11.8 - - + -
159B LEU* 3.6 3.8 - - - +
160B ALA* 2.9 49.4 + - - +
176B TYR* 1.3 76.9 - - - +
178B PHE* 1.3 73.4 + - - +
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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