Contacts of the helix formed by residues 174 - 184 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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163D ALA* 5.8 0.9 - - + -
166D PHE* 4.6 0.2 - - - -
172D GLY 3.5 5.1 - - - +
173D TRP* 1.3 88.5 - - - +
175D VAL* 1.3 65.3 + - - +
176D GLU* 3.2 15.9 - - + +
177D GLN* 3.1 43.6 + - + +
178D VAL* 3.4 5.4 + - - +
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Residues in contact with VAL 175 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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156D MSE 3.8 18.2 - - + -
161D VAL* 3.8 36.6 - - + +
163D ALA* 4.1 13.5 - - + -
166D PHE* 4.0 17.0 - - + -
173D TRP 3.7 0.2 + - - -
174D PRO* 1.3 71.8 - - - +
176D GLU* 1.3 69.0 + - - +
178D VAL* 3.0 6.0 + - - +
179D TRP* 2.9 25.1 + - - +
270D PHE* 3.6 25.8 - - + -
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Residues in contact with GLU 176 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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156D MSE 4.1 18.1 - - + +
174D PRO* 3.6 13.4 - - + +
175D VAL* 1.3 88.4 + - - +
177D GLN* 1.3 57.3 + - - +
179D TRP* 3.3 10.9 + - + +
180D LYS* 2.8 39.9 + - - +
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Residues in contact with GLN 177 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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173D TRP* 3.3 46.4 - - + +
174D PRO* 3.1 40.9 + - + +
176D GLU* 1.3 77.5 - - - +
178D VAL* 1.3 59.8 + - - +
180D LYS* 3.4 8.4 + - - +
181D GLU* 2.9 45.3 + - + +
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Residues in contact with VAL 178 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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166D PHE* 3.9 30.7 - - + -
170D ARG* 4.0 13.9 - - - -
173D TRP* 3.7 21.1 - - + -
174D PRO 3.4 5.1 + - - +
175D VAL* 3.0 8.6 + - - +
177D GLN* 1.3 74.7 - - - +
179D TRP* 1.3 56.7 + - - +
182D MSE 2.9 33.8 + - - +
266D MSE 3.3 32.0 - - + +
269D GLU* 4.3 6.1 - - + -
270D PHE* 3.5 24.9 - - + -
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Residues in contact with TRP 179 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149D LEU* 3.6 23.8 - - + -
152D ALA* 4.2 4.7 - - + -
153D GLN* 3.5 47.7 - - + +
156D MSE 3.7 38.5 - - + +
175D VAL 2.9 7.3 + - - +
176D GLU* 3.4 9.9 - - + +
178D VAL* 1.3 79.2 - - - +
180D LYS* 1.3 66.5 + - + +
182D MSE 3.5 25.1 - - + +
183D HIS* 2.7 62.7 + + - -
270D PHE* 3.6 20.8 - + + -
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Residues in contact with LYS 180 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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176D GLU* 2.8 25.9 + - - +
177D GLN* 3.9 7.9 - - - +
179D TRP* 1.3 80.1 - - + +
181D GLU* 1.3 65.9 + - + +
183D HIS* 3.3 15.0 + - - +
184D LYS* 3.6 26.2 + - - +
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Residues in contact with GLU 181 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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173D TRP* 3.9 20.3 - - + -
177D GLN* 2.9 30.1 + - + +
180D LYS* 1.3 74.8 - - + +
182D MSE 1.3 66.5 + - - +
183D HIS 3.1 1.6 - - - -
184D LYS* 2.8 57.4 + - - +
185D LEU* 3.9 8.7 + - - +
266D MSE 3.6 18.4 - - + +
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Residues in contact with MSE 182 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149D LEU* 3.6 19.3 - - + -
178D VAL 2.9 19.9 + - - +
179D TRP* 3.5 33.7 - - + +
181D GLU* 1.3 76.0 - - - +
183D HIS* 1.3 68.5 + - + +
185D LEU* 3.2 21.4 + - - +
186D LEU* 4.1 1.6 + - - +
263D PHE* 3.6 29.2 - - + -
266D MSE 3.5 25.2 - - + +
267D LEU* 3.5 41.5 - - + -
270D PHE* 3.7 16.4 - - + -
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Residues in contact with HIS 183 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149D LEU* 4.2 13.0 - - + +
179D TRP* 2.7 72.8 + + - +
180D LYS* 3.3 10.8 + - - +
181D GLU 3.1 0.8 - - - -
182D MSE 1.3 85.0 - - + +
184D LYS* 1.3 55.4 + - - +
185D LEU 3.0 5.4 - - - -
186D LEU* 3.0 48.2 + - + +
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Residues in contact with LYS 184 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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180D LYS* 3.7 25.5 - - - +
181D GLU* 2.8 46.9 + - - +
183D HIS* 1.3 76.1 - - - +
185D LEU* 1.3 65.2 + - + +
186D LEU 3.3 4.6 + - - +
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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