Contacts of the strand formed by residues 170 - 175 (chain B) in PDB entry 2Q9Q
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 TYR 170 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135A PHE* 5.3 0.2 - + - -
140A GLU 4.8 3.1 + - - -
141A ALA* 3.5 41.4 - - - +
161A THR* 3.7 31.9 + - + +
164A LEU* 3.6 46.0 - - + -
165A ASN* 2.8 24.8 + - - +
168A TYR* 4.2 21.0 - - + +
168B ASP 4.5 1.8 - - - -
169B SER* 1.3 76.8 - - - +
171B VAL* 1.3 65.0 + - - +
185B GLU 5.6 0.2 + - - -
186B PRO 4.4 2.9 + - - -
205B LEU* 4.1 9.2 - - + -
206B ILE* 3.5 23.6 - - - -
207B ARG* 3.7 26.9 + - + +
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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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161A THR* 4.7 0.4 - - - -
39B PHE* 3.8 27.1 - - + +
41B PRO* 4.9 2.0 - - + -
169B SER* 4.2 3.6 - - - +
170B TYR* 1.3 82.4 - - - +
172B PHE* 1.3 72.5 + - - +
173B LEU* 5.4 1.7 - - + +
204B HIS 3.7 0.3 - - - +
205B LEU* 3.3 5.4 - - - +
206B ILE* 2.9 37.6 + - + +
207B ARG 4.6 0.2 - - - -
208B TYR* 3.9 34.3 - - + -
211B ILE* 4.4 9.0 - - + -
222B LEU* 4.2 21.8 - - + -
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Residues in contact with PHE 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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145A LEU* 3.8 28.9 - - + -
148A LEU* 5.4 2.5 - - + -
153A ILE* 3.7 31.6 - - + -
157A GLY* 3.8 24.9 - - - -
160A LEU* 4.7 10.1 - - + -
161A THR* 3.4 28.3 - - + -
39B PHE* 5.6 1.8 - - - +
171B VAL* 1.3 76.9 - - - +
173B LEU* 1.3 62.3 + - - +
204B HIS 3.2 10.3 - - - +
205B LEU* 4.0 27.8 - - + -
222B LEU* 3.5 26.9 - - - +
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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
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171B VAL* 5.4 1.6 - - + -
172B PHE* 1.3 77.1 - - - +
174B ARG* 1.3 60.4 + - - +
175B VAL* 3.8 17.3 - - + -
198B LEU* 5.1 5.6 - - + -
203B GLN* 3.1 11.0 - - - +
204B HIS* 3.0 51.8 + - + +
206B ILE* 4.3 11.7 - - + -
211B ILE* 3.8 37.7 - - + -
220B VAL* 3.2 33.0 - - + -
221B GLN 3.0 11.7 - - - +
222B LEU* 3.9 11.2 - - + -
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Residues in contact with ARG 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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146A ASP* 4.7 6.9 + - - +
173B LEU* 1.3 74.1 - - - +
175B VAL* 1.3 68.9 + - - +
176B ARG* 3.4 2.9 + - + +
201B GLY* 3.0 32.8 + - - -
202B SER 3.5 2.0 - - - -
203B GLN* 3.0 37.1 + - + +
220B VAL* 3.4 2.2 - - - +
221B GLN* 2.6 48.9 + - + +
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Residues in contact with VAL 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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173B LEU* 3.8 17.3 - - + -
174B ARG* 1.3 72.5 - - - +
176B ARG* 1.3 62.1 + - - +
177B GLU 3.4 22.9 - - - +
179B GLN* 5.4 0.9 - - + -
198B LEU* 3.6 27.6 - - + +
199B GLU 3.0 35.4 - - - +
200B LYS* 3.7 4.0 - - - +
201B GLY* 2.8 27.7 + - - -
202B SER* 2.9 24.3 + - - +
204B HIS* 3.9 2.7 - - + -
219B ALA 4.3 1.6 - - - +
220B VAL* 3.8 8.5 - - + -
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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