Contacts of the helix formed by residues 179 - 184 (chain B) in PDB entry 1XV9
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 LEU 179 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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116B THR* 4.6 11.7 - - + +
117B LEU* 5.3 7.4 - - + -
120B ALA* 4.3 7.4 - - + -
175B PHE* 3.5 24.9 - - + +
176B THR* 3.2 32.5 - - + +
177B LYS 3.0 3.4 + - - -
178B ASP* 1.3 94.6 - - - +
180B PRO* 1.3 68.3 - - + +
181B VAL* 4.6 1.6 - - + +
182B PHE* 3.6 19.3 - - + +
183B ARG* 2.9 34.7 + - - +
267B LEU* 4.4 15.0 - - + -
268B PHE* 5.0 7.0 - - + -
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Residues in contact with PRO 180 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116B THR* 4.4 17.5 - - + -
178B ASP 4.3 4.5 - - - +
179B LEU* 1.3 85.2 - - + +
181B VAL* 1.3 61.3 + - + +
183B ARG* 3.4 4.1 + - + +
184B SER* 2.8 36.1 + - - -
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Residues in contact with VAL 181 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113B LEU* 6.3 3.1 - - + -
179B LEU* 3.3 1.5 - - + -
180B PRO* 1.3 81.5 - - + +
182B PHE* 1.3 64.4 + - - +
184B SER* 3.2 18.8 + - - +
185B LEU* 3.4 12.6 - - - +
268B PHE* 4.4 10.3 - - + -
280B GLU* 4.4 6.7 - - - +
284B LEU* 3.4 45.1 - - + -
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Residues in contact with PHE 182 (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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176B THR* 3.3 45.3 - - - +
179B LEU* 3.5 16.6 + - + +
180B PRO 3.4 0.6 - - - -
181B VAL* 1.3 74.0 - - - +
183B ARG* 1.3 63.6 + - - +
184B SER 2.9 4.9 - - - -
185B LEU* 3.0 20.7 + - + +
190B GLN* 3.2 76.2 - - + +
193B LEU* 3.4 31.4 - - + -
194B LEU* 3.9 14.4 - - + -
267B LEU* 4.0 14.1 - - + -
268B PHE* 3.7 22.3 - + + -
694F LEU* 4.7 2.7 - - + -
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Residues in contact with ARG 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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176B THR 4.2 1.8 - - - +
177B LYS* 3.2 56.5 + - - +
179B LEU 2.9 22.4 + - - +
180B PRO* 3.7 4.7 - - + +
182B PHE* 1.3 77.0 - - - +
184B SER* 1.3 58.4 + - - +
185B LEU 3.2 6.6 + - - +
187B ILE* 4.9 1.0 - - - +
190B GLN* 3.4 32.1 + - - +
694F LEU* 2.9 24.2 + - - +
695F GLN 3.0 29.3 + - - -
696F GLU* 3.6 14.3 + - - +
697F GLY 5.0 0.4 - - - +
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Residues in contact with SER 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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180B PRO 2.8 18.5 + - - -
181B VAL* 3.2 15.2 + - - +
182B PHE 2.9 0.6 - - - -
183B ARG* 1.3 77.2 - - - +
185B LEU* 1.3 60.2 + - - +
186B PRO* 4.1 3.3 - - - +
280B GLU* 3.8 15.8 + - - +
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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