Contacts of the strand formed by residues 170 - 177 (chain B) in PDB entry 1Q99
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 SER 170 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144B TYR* 3.4 16.3 - - - -
167B GLY* 2.9 26.9 + - - -
168B HIS 3.5 0.6 - - - -
169B PHE* 1.3 81.2 - - - +
171B THR* 1.3 61.1 + - - +
172B VAL* 4.2 3.4 + - - +
187B LYS* 3.5 23.3 - - - +
188B ILE 2.9 30.7 - - - -
189B VAL* 3.6 7.9 - - - -
902B ANP 3.5 15.1 + - - -
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Residues in contact with THR 171 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144B TYR* 4.1 15.0 - - + -
145B HIS 4.3 16.2 - - - +
163B LYS* 3.2 30.7 + - - +
165B GLY 4.0 3.1 + - - -
166B TRP* 4.0 15.2 + - - +
170B SER* 1.3 75.7 - - - +
172B VAL* 1.3 60.2 + - - +
173B TRP* 3.7 14.9 + - - +
186B MET 3.6 1.2 - - - +
187B LYS* 3.6 0.2 - - - -
188B ILE* 2.8 49.5 + - + +
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Residues in contact with VAL 172 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163B LYS* 3.6 4.2 - - - +
164B LEU* 2.7 34.5 + - + -
165B GLY 2.7 19.5 + - - +
170B SER* 4.3 6.7 - - - +
171B THR* 1.3 76.8 + - - +
173B TRP* 1.3 60.8 + - - +
185B ALA* 4.4 4.5 - - + -
186B MET 3.3 12.1 - - - +
187B LYS* 3.5 24.2 - - + -
902B ANP 3.1 65.5 - - + +
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Residues in contact with TRP 173 (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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145B HIS 5.2 0.2 + - - -
147B ALA* 3.3 45.9 - - + +
148B PHE* 4.0 4.3 - - - -
149B LYS* 4.0 15.7 - - + -
160B LEU* 3.6 42.2 - - + -
162B ARG* 3.4 28.9 - - - -
163B LYS* 3.7 34.4 - - + +
164B LEU* 3.9 4.8 - - - +
171B THR* 3.7 25.0 + - + +
172B VAL* 1.3 79.9 - - - +
174B LEU* 1.3 61.1 + - - +
175B ALA 3.9 0.2 + - - -
185B ALA* 3.3 4.9 - - - -
186B MET* 2.8 40.8 + - + +
188B ILE* 3.8 19.3 - - + -
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Residues in contact with LEU 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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160B LEU* 3.7 1.9 - - - -
161B VAL* 2.8 39.3 + - + -
162B ARG* 2.7 51.3 + - - +
164B LEU* 3.6 20.3 - - + +
173B TRP* 1.3 73.4 - - - +
175B ALA* 1.3 61.1 + - - +
183B HIS* 4.0 22.7 - - + -
184B VAL 3.6 15.9 - - - +
248B VAL* 3.6 27.8 - - + -
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Residues in contact with ALA 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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158B TYR* 4.3 4.7 - - + -
159B ILE 3.5 18.4 - - - +
160B LEU* 4.0 6.1 - - + -
161B VAL* 4.0 5.6 - - - -
173B TRP 3.9 0.2 + - - -
174B LEU* 1.3 76.3 - - - +
176B LYS* 1.3 60.7 + - - +
183B HIS* 3.3 7.2 - - - +
184B VAL* 2.9 37.8 + - + -
186B MET* 4.1 33.4 - - + -
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Residues in contact with LYS 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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158B TYR* 3.3 3.3 - - - -
159B ILE* 3.0 38.5 + - + +
161B VAL* 3.9 10.5 - - + +
175B ALA* 1.3 74.3 - - - +
177B ASP* 1.3 59.3 + - - +
178B MET* 3.1 35.5 + - - +
181B ASN* 3.1 44.1 + - - +
182B THR 3.7 5.9 + - - +
183B HIS* 4.2 23.9 - - + +
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Residues in contact with ASP 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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157B ARG* 3.3 21.9 + - - +
158B TYR* 3.5 21.6 + - + -
175B ALA 3.8 2.2 + - - -
176B LYS* 1.3 69.4 - - - +
178B MET* 1.3 57.7 + - - +
179B VAL* 2.7 28.9 + - - +
180B ASN* 2.6 34.6 + - - -
181B ASN* 2.8 23.0 + - - -
182B THR* 2.8 26.3 + - - +
184B VAL* 4.2 10.7 - - + +
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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