Contacts of the strand formed by residues 182 - 189 (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 THR 182 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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176B LYS* 3.7 5.4 - - - +
177B ASP* 2.8 30.1 + - - +
180B ASN* 3.1 33.7 + - + +
181B ASN* 1.3 79.9 - - - +
183B HIS* 1.3 78.3 + - - +
184B VAL* 4.2 4.3 - - - +
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Residues in contact with HIS 183 (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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161B VAL* 4.6 7.9 - - + +
174B LEU* 4.0 32.1 - - + -
175B ALA 3.3 17.3 - - - +
176B LYS* 4.2 31.7 - - + +
182B THR* 1.3 82.6 + - - +
184B VAL* 1.3 72.2 + - - +
247B GLU* 4.9 2.1 - - - +
248B VAL* 3.7 14.4 + - + +
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Residues in contact with VAL 184 (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* 3.7 26.7 - - + -
174B LEU* 3.6 2.4 - - - +
175B ALA* 2.9 40.5 + - + +
177B ASP* 4.2 15.0 - - + +
180B ASN* 5.9 0.9 - - - +
182B THR* 4.2 10.1 - - - +
183B HIS* 1.3 82.1 - - - +
185B ALA* 1.3 60.1 + - - +
186B MET* 4.0 10.5 - - + -
229B LEU* 4.6 10.5 - - + -
245B VAL* 3.7 20.6 - - + -
246B PHE 3.3 12.6 - - - +
247B GLU* 5.1 0.9 - - - -
248B VAL* 3.3 15.1 - - - +
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Residues in contact with ALA 185 (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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164B LEU* 4.0 15.3 - - + -
172B VAL* 4.4 4.3 - - + -
173B TRP 3.3 5.6 - - - +
184B VAL* 1.3 73.5 - - - +
186B MET* 1.3 62.0 + - - +
244B MET 3.7 0.7 - - - +
245B VAL* 3.4 2.1 - - - -
246B PHE* 2.8 40.7 + - + +
247B GLU 4.0 2.0 - - - +
248B VAL* 3.7 3.1 - - + +
902B ANP 3.7 41.1 - - + +
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Residues in contact with MET 186 (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 TYR* 3.7 28.3 - - + -
158B TYR* 3.6 37.9 - - + -
160B LEU* 3.6 29.2 - - + -
171B THR 3.6 1.4 - - - +
172B VAL* 3.3 2.5 - - - -
173B TRP* 2.8 43.3 + - + +
175B ALA* 4.1 8.5 - - + -
184B VAL* 4.0 13.5 - - + -
185B ALA* 1.3 77.8 - - - +
187B LYS* 1.3 63.6 + - - +
188B ILE* 3.7 5.5 + - + +
232B PHE* 4.4 0.2 - - - -
243B VAL* 4.1 12.8 - - + -
244B MET 3.2 6.7 - - - +
245B VAL* 3.7 16.4 - - + -
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Residues in contact with LYS 187 (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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170B SER* 3.5 10.8 - - - +
171B THR 3.6 3.8 - - - -
172B VAL* 3.5 25.1 - - + -
186B MET* 1.3 73.2 - - - +
188B ILE* 1.3 62.9 + - - +
189B VAL* 3.6 4.4 + - - +
202B GLU* 3.4 25.3 + - - -
242B VAL 3.8 0.5 - - - +
243B VAL* 3.4 4.2 - - - -
244B MET* 2.7 44.2 + - + +
246B PHE* 3.3 29.6 - - + -
550B ASP* 4.2 10.7 + - - +
902B ANP 2.8 57.2 + - + +
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Residues in contact with ILE 188 (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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144B TYR* 5.0 1.7 - - - -
145B HIS* 4.0 29.9 + - + +
147B ALA* 4.3 6.7 - - + -
153B TYR* 3.5 32.3 - - + +
160B LEU* 4.7 4.7 - - + -
170B SER* 2.9 17.5 - - - -
171B THR* 2.8 31.8 + - + +
173B TRP* 3.8 27.4 - - + +
186B MET* 4.3 7.4 - - + +
187B LYS* 1.3 71.6 - - - +
189B VAL* 1.3 63.3 + - - +
241B HIS* 4.1 16.6 - - + -
242B VAL 3.9 2.5 - - - -
243B VAL* 4.2 19.5 - - + -
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Residues in contact with VAL 189 (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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144B TYR* 5.7 0.9 - - - -
169B PHE* 3.4 23.1 - - + +
170B SER* 3.6 7.4 - - - -
187B LYS 4.2 3.6 - - - +
188B ILE* 1.3 75.2 - - - +
190B ARG* 1.3 78.1 + - - +
195B TYR* 3.8 26.2 - - + +
196B THR* 4.8 0.9 - - - +
199B ALA* 3.9 12.3 - - + -
241B HIS* 2.9 24.1 + - - +
242B VAL* 3.0 24.9 + - + +
244B MET* 3.6 30.7 - - + -
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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