Contacts of the helix formed by residues 191 - 200 (chain P) in PDB entry 5D4D
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 ASN 191 (chain P).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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93P LEU* 5.2 0.7 - - - +
94P LEU* 4.7 4.5 - - - +
99P GLU* 4.9 1.6 - - - +
187P LEU* 2.8 35.9 + - - +
188P ILE 3.3 3.0 + - - -
190P ALA* 1.3 80.9 - - - +
192P LEU* 1.3 61.5 + - - +
193P ARG 3.0 5.6 + - - -
194P LEU* 3.1 20.0 + - + +
195P VAL 3.9 0.3 + - - -
220P LEU* 3.5 28.4 - - + +
235P PHE* 3.2 33.3 - - + +
6S T 2.9 38.6 + - - +
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Residues in contact with LEU 192 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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563N PRO* 5.9 0.2 - - + -
565N ILE* 4.0 28.9 - - + -
566N ILE* 3.9 16.2 - - + -
84P TYR* 3.6 5.6 + - - +
88P ILE* 3.7 35.1 - - + +
188P ILE* 3.6 11.6 + - + +
189P GLU* 3.8 22.9 - - + +
190P ALA 3.4 3.0 + - - -
191P ASN* 1.3 76.1 - - - +
193P ARG* 1.3 62.0 + - + +
195P VAL* 3.4 13.9 + - - +
196P VAL* 3.5 13.5 + - - +
217P ASN* 3.4 38.4 - - - +
220P LEU* 4.1 7.9 - - + -
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Residues in contact with ARG 193 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88P ILE* 3.6 24.7 + - + +
89P GLY* 3.4 25.3 + - - -
91P VAL 3.2 28.3 + - - -
92P PRO* 4.4 4.9 - - - +
93P LEU* 3.5 40.0 - - - +
190P ALA 4.6 3.2 + - - -
191P ASN 3.0 1.0 + - - -
192P LEU* 1.3 74.5 - - + +
194P LEU* 1.3 65.9 + - - +
196P VAL* 3.0 5.7 + - - +
197P SER* 3.0 22.9 + - - -
6S T 3.4 21.1 - - - +
7S G 3.2 52.9 + - + +
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Residues in contact with LEU 194 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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191P ASN* 3.1 9.9 + - + +
193P ARG* 1.3 74.6 - - - +
195P VAL* 1.3 57.7 + - - +
197P SER* 2.7 19.8 + - - +
198P ILE* 2.9 27.3 + - + +
220P LEU* 5.0 2.9 - - + -
235P PHE* 5.5 0.4 - - + -
236P SER* 3.9 25.1 - - - -
239P ALA* 3.9 9.2 - - + -
240P THR* 3.7 23.3 - - - +
243P ILE* 3.7 24.0 - - + -
5S A 4.0 24.2 - - + -
6S T 3.1 40.1 + - + +
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Residues in contact with VAL 195 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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192P LEU 3.6 7.0 - - - +
193P ARG 3.2 0.4 - - - -
194P LEU* 1.3 75.4 - - - +
196P VAL* 1.3 58.7 + - + +
198P ILE* 3.4 1.4 + - - +
199P ALA* 2.9 28.2 + - + +
213P ILE* 3.3 24.5 - - + +
216P GLY* 3.5 19.1 - - - +
217P ASN* 3.2 28.0 - - - +
220P LEU* 3.7 28.9 - - + -
243P ILE* 3.6 30.6 - - + +
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Residues in contact with VAL 196 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84P TYR* 3.7 18.4 - - + -
85P LEU* 3.9 7.9 - - + -
88P ILE* 3.7 25.6 - - + -
192P LEU 3.5 4.0 + - - +
193P ARG 3.0 9.7 + - - +
195P VAL* 1.3 78.0 - - - +
197P SER* 1.3 58.8 + - - +
199P ALA* 3.2 1.2 + - - +
200P LYS* 2.9 30.7 + - - +
209P PHE* 4.2 5.7 - - + -
213P ILE* 3.9 20.2 - - + -
7S G 3.7 24.7 - - - -
8S G 3.9 21.5 - - - +
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Residues in contact with SER 197 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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193P ARG 3.0 7.9 + - - -
194P LEU* 2.7 32.1 + - - +
196P VAL* 1.3 78.4 - - - +
198P ILE* 1.3 57.6 + - - +
200P LYS* 3.2 44.0 - - - +
201P LYS* 3.6 11.2 - - - -
6S T 3.6 23.0 - - - -
7S G 4.6 8.5 - - - -
8S G 5.4 0.7 - - - -
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Residues in contact with ILE 198 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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194P LEU* 2.9 25.1 + - + +
195P VAL 3.8 3.8 - - - +
197P SER* 1.3 78.8 - - - +
199P ALA* 1.3 61.4 + - - +
201P LYS* 3.4 22.0 + - - +
202P TYR* 3.1 28.3 - - + -
240P THR* 3.5 38.1 - - + +
243P ILE* 3.6 43.7 - - + -
244P ARG* 3.9 22.0 - - + +
247P ILE* 3.8 9.0 - - + -
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Residues in contact with ALA 199 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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195P VAL 2.9 18.6 + - - +
196P VAL 3.9 2.7 - - - +
198P ILE* 1.3 72.4 - - - +
200P LYS* 1.3 58.0 + - - +
201P LYS 3.0 6.3 - - - -
202P TYR* 2.9 18.9 + - - -
203P THR* 3.9 1.6 + - - +
209P PHE* 4.2 5.5 - - + -
212P LEU* 3.6 32.1 - - + +
213P ILE* 4.0 20.4 - - + +
247P ILE* 3.7 19.3 - - + -
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Residues in contact with LYS 200 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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353M ARG* 4.1 1.4 + - - -
357M GLU* 4.0 5.0 - - - +
196P VAL 2.9 11.2 + - - +
197P SER* 3.2 39.4 - - - +
199P ALA* 1.3 76.2 - - - +
201P LYS* 1.3 64.6 + - + +
202P TYR 3.3 0.2 - - - -
203P THR* 3.3 21.5 + - - +
209P PHE* 4.0 10.3 - - + -
7S G 5.8 1.8 + - - -
8S G 3.5 55.0 + - - +
9S G 4.2 14.8 + - - +
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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