Contacts of the helix formed by residues 174 - 184 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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163A ALA* 6.1 0.4 - - + -
172A GLY 3.5 7.4 - - - +
173A TRP* 1.3 85.7 - - - +
175A VAL* 1.3 65.0 + - - +
176A GLU* 3.5 17.7 - - + +
177A GLN* 2.9 39.5 + - + +
178A VAL* 3.2 9.1 + - - +
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Residues in contact with VAL 175 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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156A MSE 3.8 22.9 - - + +
161A VAL* 3.8 25.6 - - + -
163A ALA* 5.2 8.3 - - + +
166A PHE* 4.2 17.8 - - + -
173A TRP 3.5 2.6 + - - -
174A PRO* 1.3 70.2 - - - +
176A GLU* 1.3 79.1 + - - +
178A VAL* 3.2 4.5 + - + +
179A TRP* 2.9 26.5 + - - +
270A PHE* 3.7 25.4 - - + -
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Residues in contact with GLU 176 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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156A MSE 4.3 16.4 - - + +
174A PRO* 3.5 18.9 - - + +
175A VAL* 1.3 94.7 + - + +
177A GLN* 1.3 56.6 + - - +
179A TRP* 3.4 3.7 + - - +
180A LYS* 2.9 37.6 + - + +
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Residues in contact with GLN 177 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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173A TRP* 3.8 41.3 - - + +
174A PRO* 2.9 36.8 + - + +
176A GLU* 1.3 76.2 - - - +
178A VAL* 1.3 65.3 + - - +
180A LYS* 3.9 6.0 - - + -
181A GLU* 2.9 43.2 + - + +
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Residues in contact with VAL 178 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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166A PHE* 3.8 30.5 - - + -
170A ARG* 4.1 22.2 - - - -
173A TRP* 3.8 24.4 - - + -
174A PRO 3.2 7.6 + - - +
175A VAL* 3.2 8.2 + - - +
177A GLN* 1.3 74.2 - - - +
179A TRP* 1.3 63.0 + - - +
182A MSE 3.0 26.7 + - - +
266A MSE 3.6 19.0 - - + +
269A GLU* 4.3 8.3 - - + -
270A PHE* 3.7 23.1 - - + -
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Residues in contact with TRP 179 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149A LEU* 3.5 32.3 - - + -
152A ALA* 4.0 5.4 - - + -
153A GLN* 3.6 42.6 - - + +
156A MSE 3.6 29.8 - - + +
175A VAL 2.9 12.9 + - - +
176A GLU* 3.5 9.6 - - - +
178A VAL* 1.3 78.2 - - - +
180A LYS* 1.3 70.7 + - + +
182A MSE 3.4 35.3 + - + +
183A HIS* 2.9 51.6 + + - -
270A PHE* 3.6 21.4 - + + -
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Residues in contact with LYS 180 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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176A GLU* 2.9 25.4 + - + +
177A GLN* 4.0 7.0 - - + +
179A TRP* 1.3 86.5 - - + +
181A GLU* 1.3 63.9 + - + +
183A HIS* 3.2 15.9 + - - +
184A LYS* 3.7 22.4 + - - +
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Residues in contact with GLU 181 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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173A TRP* 3.6 24.4 - - + -
177A GLN* 2.9 34.0 + - + +
180A LYS* 1.3 74.9 - - + +
182A MSE 1.3 68.0 + - - +
184A LYS* 2.7 55.2 + - - +
185A LEU* 4.1 7.6 + - - +
266A MSE 3.6 18.5 - - + +
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Residues in contact with MSE 182 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149A LEU* 3.5 19.3 - - + -
178A VAL 3.0 18.9 + - - +
179A TRP* 3.5 35.2 - - + +
180A LYS 3.2 0.2 - - - -
181A GLU* 1.3 79.1 - - - +
183A HIS* 1.3 65.7 + - + +
184A LYS 3.3 0.9 + - - -
185A LEU* 3.3 18.3 + - + +
186A LEU* 4.2 2.4 + - - +
263A PHE* 3.8 28.2 - - + -
266A MSE 3.6 26.9 - - + +
267A LEU* 3.6 42.0 - - + -
270A PHE* 3.5 15.5 - - + -
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Residues in contact with HIS 183 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149A LEU* 4.2 12.7 - - + +
179A TRP* 2.9 72.8 + + - -
180A LYS* 3.2 10.5 + - - +
181A GLU 3.2 1.2 - - - -
182A MSE 1.3 85.4 - - + +
184A LYS* 1.3 61.5 + - - +
185A LEU 3.2 1.1 + - - -
186A LEU* 3.4 37.2 + - + +
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Residues in contact with LYS 184 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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180A LYS* 3.8 20.9 - - - +
181A GLU* 2.7 42.8 + - - +
183A HIS* 1.3 78.9 - - - +
185A LEU* 1.3 61.6 + - + +
186A LEU 3.4 4.8 + - - +
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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