Contacts of the helix formed by residues 185 - 195 (chain D) in PDB entry 4GCK
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 ASP 185 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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157C LEU* 4.4 8.7 - - + -
183D THR 3.0 1.8 + - - -
184D ASP* 1.3 80.9 - - - +
186D PHE* 1.3 67.3 + - - +
187D GLU* 3.2 3.4 - - - +
188D ALA* 2.8 19.4 + - + +
189D ARG* 2.8 37.7 + - + +
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Residues in contact with PHE 186 (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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89D ARG* 3.7 43.3 - - + -
92D VAL* 3.9 23.3 - - + -
93D LEU* 3.7 39.7 - - + -
96D LEU* 4.1 17.7 - - + -
165D PHE* 4.9 6.5 - + - -
182D PRO 5.3 0.9 - - - -
183D THR* 3.0 24.8 + - - +
184D ASP 3.1 3.0 - - - -
185D ASP* 1.3 76.2 - - - +
187D GLU* 1.3 75.9 + - - +
189D ARG* 3.0 6.0 + - - +
190D TRP* 2.7 57.9 + + + +
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Residues in contact with GLU 187 (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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89D ARG* 2.8 31.8 + - - -
93D LEU* 5.4 2.1 - - - +
185D ASP* 3.2 1.5 - - - -
186D PHE* 1.3 94.1 - - - +
188D ALA* 1.3 57.3 + - - +
190D TRP* 4.9 1.6 - - - -
191D PRO* 3.1 24.9 - - - +
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Residues in contact with ALA 188 (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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153C LEU* 5.9 1.4 - - - +
157C LEU* 4.0 21.4 - - + +
185D ASP* 2.8 22.2 + - + +
187D GLU* 1.3 79.7 - - - +
189D ARG* 1.3 62.0 + - - +
190D TRP 3.6 0.2 - - - -
191D PRO* 3.5 8.7 - - - +
192D LEU* 3.8 18.5 - - - +
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Residues in contact with ARG 189 (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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157C LEU* 3.5 28.1 + - + +
160C SER* 3.0 34.7 + - - -
161C GLN* 2.9 36.7 + - - +
165D PHE* 4.2 14.1 - - + -
169D MET* 3.7 30.9 - - - +
172D ARG* 6.1 0.2 - - - +
182D PRO 5.4 0.7 - - - -
184D ASP* 3.4 22.5 + - - +
185D ASP* 2.8 23.0 + - - +
186D PHE* 3.7 6.7 - - + +
188D ALA* 1.3 78.4 - - - +
190D TRP* 1.3 65.8 + - - +
192D LEU* 2.9 21.0 + - - +
193D VAL* 3.0 14.2 + - - +
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Residues in contact with TRP 190 (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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85D THR* 3.9 19.5 - - + +
88D LEU* 3.8 13.0 - - + -
89D ARG* 3.4 66.6 - - + +
92D VAL* 4.0 21.1 - - + -
162D LEU* 4.8 2.7 - - + -
165D PHE* 5.5 0.4 - + - -
186D PHE* 2.7 47.8 + + + +
187D GLU* 4.9 1.3 - - - +
189D ARG* 1.3 73.2 - - - +
191D PRO* 1.3 67.9 - - + +
193D VAL* 3.1 28.1 + - + +
194D ALA* 2.8 47.0 + - + +
197D LEU* 4.5 10.1 - - + -
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Residues in contact with PRO 191 (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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198C GLN* 4.7 2.7 + - - +
187D GLU 3.1 25.6 - - - +
188D ALA* 3.5 6.7 - - - +
189D ARG 3.4 4.0 - - - -
190D TRP* 1.3 97.5 - - + +
192D LEU* 1.3 62.4 + - + +
194D ALA* 3.5 8.8 + - + +
195D ALA* 3.1 26.0 + - - +
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Residues in contact with LEU 192 (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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153C LEU* 3.5 23.3 - - + -
157C LEU* 4.1 16.6 - - + -
158C LEU* 3.8 26.0 - - + -
161C GLN* 4.0 13.9 - - + +
196C GLN* 3.0 47.4 - - + +
198C GLN* 4.1 11.7 - - - +
188D ALA 3.8 19.1 - - - +
189D ARG* 2.9 10.0 + - - +
191D PRO* 1.3 81.2 - - + +
193D VAL* 1.3 65.8 + - - +
195D ALA* 3.2 16.8 + - - +
196D GLN 3.8 0.9 + - - -
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Residues in contact with VAL 193 (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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161C GLN* 3.4 22.7 - - - +
196C GLN* 4.1 1.6 - - - +
92D VAL* 5.9 0.2 - - + -
162D LEU* 3.5 28.0 - - + -
165D PHE* 3.9 39.3 - - + -
189D ARG 3.0 9.6 + - - +
190D TRP* 3.6 24.0 - - + +
192D LEU* 1.3 75.6 - - - +
194D ALA* 1.3 57.2 + - - +
196D GLN* 3.0 41.0 + - - +
197D LEU* 4.0 5.2 + - - +
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Residues in contact with ALA 194 (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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85D THR* 4.7 10.3 - - + -
190D TRP* 2.8 41.1 + - + +
191D PRO* 3.7 9.0 - - + +
193D VAL* 1.3 72.1 - - - +
195D ALA* 1.3 61.7 + - - +
196D GLN 3.0 5.8 - - - -
197D LEU* 3.0 31.9 + - + +
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Residues in contact with ALA 195 (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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195C ALA* 3.8 15.7 - - + +
198C GLN* 3.7 22.2 - - - +
191D PRO 3.1 13.1 + - - +
192D LEU 3.4 12.3 - - - +
193D VAL 3.1 0.8 - - - -
194D ALA* 1.3 77.2 - - - +
196D GLN* 1.3 58.5 + - - +
197D LEU 3.3 0.7 - - - -
198D GLN* 3.0 27.1 + - - +
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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