Contacts of the helix formed by residues 174 - 184 (chain B) in PDB entry 4GKH
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 PRO 174 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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163B ALA* 6.2 0.2 - - + -
172B GLY 3.5 5.1 - - - +
173B TRP* 1.3 89.0 - - - +
175B VAL* 1.3 65.2 + - - +
176B GLU* 4.3 9.4 - - + +
177B GLN* 3.0 37.9 + - + +
178B VAL* 3.4 8.7 + - - +
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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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156B MSE 3.7 22.0 - - + -
161B VAL* 4.0 34.5 - - + +
163B ALA* 4.2 14.8 - - + +
166B PHE* 4.1 16.2 - - + -
173B TRP 3.6 1.0 + - - -
174B PRO* 1.3 70.3 - - - +
176B GLU* 1.3 62.7 + - - +
178B VAL* 3.1 6.2 + - - +
179B TRP* 3.0 19.1 + - - +
270B PHE* 3.7 24.6 - - + -
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Residues in contact with GLU 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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156B MSE 3.7 23.4 - - - +
174B PRO* 3.2 7.1 - - + +
175B VAL* 1.3 81.6 - - - +
177B GLN* 1.3 56.3 + - - +
179B TRP* 3.4 15.3 + - - +
180B LYS* 3.0 68.1 + - - +
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Residues in contact with GLN 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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173B TRP* 3.6 44.1 - - + +
174B PRO* 3.0 38.1 + - + +
176B GLU* 1.3 76.7 - - - +
178B VAL* 1.3 64.7 + - - +
180B LYS* 3.5 6.6 + - + +
181B GLU* 3.1 42.6 + - + +
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Residues in contact with VAL 178 (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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166B PHE* 3.7 35.4 - - + -
170B ARG* 4.1 13.0 - - - -
173B TRP* 3.9 21.3 - - + -
174B PRO 3.8 7.4 - - - +
175B VAL* 3.1 7.5 + - - +
177B GLN* 1.3 76.4 - - - +
179B TRP* 1.3 62.4 + - - +
182B MSE 3.0 27.9 + - - +
266B MSE 3.5 24.6 - - + +
269B GLU* 4.2 6.7 - - + -
270B PHE* 3.6 24.7 - - + -
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Residues in contact with TRP 179 (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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149B LEU* 3.6 31.0 - - + -
152B ALA* 4.1 5.6 - - + -
153B GLN* 3.6 43.5 - - + +
156B MSE 3.7 33.8 - - + +
175B VAL 3.0 6.8 + - - +
176B GLU* 3.5 26.2 - - - +
178B VAL* 1.3 78.6 - - - +
180B LYS* 1.3 62.0 + - + +
182B MSE 3.6 24.1 + - + +
183B HIS* 2.8 62.5 + + - -
270B PHE* 3.6 21.2 - + + -
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Residues in contact with LYS 180 (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 GLU* 3.0 51.7 + - - +
177B GLN* 4.1 6.1 - - + +
179B TRP* 1.3 78.2 - - + +
181B GLU* 1.3 66.5 + - + +
183B HIS* 3.1 16.9 + - - +
184B LYS* 3.6 22.3 + - - +
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Residues in contact with GLU 181 (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 TRP* 3.5 25.1 - - + -
177B GLN* 3.1 31.6 + - + +
180B LYS* 1.3 77.7 - - + +
182B MSE 1.3 64.4 + - - +
184B LYS* 3.2 43.8 + - - +
185B LEU* 4.0 7.6 + - - +
266B MSE 3.7 16.6 - - + +
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Residues in contact with MSE 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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149B LEU* 3.6 23.1 - - + -
178B VAL 3.0 19.7 + - - +
179B TRP* 3.7 28.7 - - + +
180B LYS 3.3 0.2 - - - -
181B GLU* 1.3 77.7 - - - +
183B HIS* 1.3 67.1 + - + +
185B LEU* 3.1 21.2 + - - +
186B LEU* 4.1 1.0 + - - +
263B PHE* 3.6 28.5 - - + -
266B MSE 3.4 26.8 - - + +
267B LEU* 3.5 42.0 - - + -
270B PHE* 3.7 15.5 - - + -
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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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149B LEU* 4.2 13.1 - - + +
179B TRP* 2.8 72.2 + + - +
180B LYS* 3.1 12.9 + - - +
182B MSE 1.3 81.9 - - + +
184B LYS* 1.3 63.7 + - - +
185B LEU 3.1 2.2 - - - -
186B LEU* 3.3 39.8 + - + +
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Residues in contact with LYS 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 LYS* 3.6 15.9 + - - +
181B GLU* 3.3 45.0 + - - +
182B MSE 3.1 0.8 - - - -
183B HIS* 1.3 78.1 - - - +
185B LEU* 1.3 63.4 + - + +
186B LEU 3.3 5.5 + - - +
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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