Contacts of the helix formed by residues 191 - 205 (chain P) in PDB entry 1SVC
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 191 (chain P).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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190P GLY* 1.3 72.6 - - - -
192P ARG* 1.3 63.4 + - - +
194P LYS* 3.2 22.5 + - - +
195P GLU* 3.1 23.0 + - - +
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Residues in contact with ARG 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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175P ASP* 3.8 17.8 + - - +
176P LEU* 5.6 0.2 - - - +
178P TYR* 4.8 5.8 + - - +
190P GLY 3.3 1.0 - - - -
191P ASP* 1.3 80.2 - - - +
193P GLU* 1.3 76.9 + - - +
194P LYS 3.1 0.2 + - - -
195P GLU* 3.2 13.1 + - - +
196P LEU* 3.2 47.8 + - + +
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Residues in contact with GLU 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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176P LEU* 4.3 16.7 - - + +
178P TYR* 2.9 27.7 + - - -
179P LEU* 3.9 28.7 - - + +
188P GLN 4.1 7.6 - - - +
189P LEU* 3.9 20.9 - - + +
190P GLY* 3.1 33.4 + - - +
192P ARG* 1.3 83.1 - - - +
194P LYS* 1.3 56.0 + - - +
196P LEU* 3.2 4.6 + - - +
197P ILE* 3.0 35.0 + - + +
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Residues in contact with LYS 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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155P GLU* 5.4 0.9 - - - +
186P ASP* 5.1 10.7 + - - +
189P LEU* 3.6 37.8 + - + -
190P GLY 3.1 20.7 + - - +
191P ASP* 3.3 20.9 + - - +
192P ARG 3.1 0.8 - - - -
193P GLU* 1.3 77.4 - - - +
195P GLU* 1.3 64.5 + - - +
197P ILE* 3.1 11.7 + - - +
198P ARG* 3.0 20.4 + - - +
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Residues in contact with GLU 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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191P ASP 3.1 12.6 + - - +
192P ARG* 3.9 8.1 - - - +
194P LYS* 1.3 76.8 - - - +
196P LEU* 1.3 57.4 + - - +
198P ARG* 3.1 30.6 + - - +
199P GLN* 2.9 55.7 + - + +
202P LEU* 5.9 0.2 - - - +
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Residues in contact with LEU 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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172P VAL* 4.7 2.9 - - - +
173P HIS* 3.5 33.9 + - + +
175P ASP* 4.0 13.5 - - + -
176P LEU* 3.4 37.5 - - + -
192P ARG* 3.2 52.1 + - - +
193P GLU 3.2 9.3 + - - +
194P LYS 3.2 0.4 - - - -
195P GLU* 1.3 76.0 - - - +
197P ILE* 1.3 62.2 + - - +
199P GLN* 3.3 13.8 + - + +
200P ALA* 3.1 24.8 + - - +
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Residues in contact with ILE 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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155P GLU* 3.6 21.8 - - + +
158P MET* 3.5 26.5 - - + +
159P THR* 3.7 22.7 - - - +
162P CYS* 3.5 36.6 - - + -
172P VAL* 4.3 12.6 - - + -
176P LEU* 4.3 1.8 - - + -
189P LEU* 3.9 17.9 - - + -
193P GLU 3.0 21.1 + - - +
194P LYS* 3.1 8.7 + - - +
196P LEU* 1.3 76.8 - - - +
198P ARG* 1.3 64.9 + - - +
200P ALA 3.5 0.2 + - - -
201P ALA* 3.1 22.5 + - - +
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Residues in contact with ARG 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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151P PHE* 3.6 33.1 - - + -
155P GLU* 3.8 24.4 + - - +
194P LYS 3.0 12.3 + - - +
195P GLU* 3.1 33.4 + - - +
197P ILE* 1.3 78.1 - - - +
199P GLN* 1.3 56.9 + - - +
201P ALA* 3.5 2.2 + - - +
202P LEU* 3.1 54.7 + - + +
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Residues in contact with GLN 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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173P HIS* 6.1 1.1 - - - +
195P GLU* 2.9 47.6 + - + +
196P LEU* 3.3 17.0 + - + +
198P ARG* 1.3 78.4 - - - +
200P ALA* 1.3 60.3 + - - +
202P LEU* 4.1 16.2 - - - +
203P GLN* 3.3 23.4 + - - +
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Residues in contact with ALA 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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158P MET* 3.5 22.2 - - + -
172P VAL* 3.6 24.2 - - + +
173P HIS* 5.3 4.7 - - + +
196P LEU 3.1 16.1 + - - +
197P ILE 4.0 0.9 - - - +
199P GLN* 1.3 73.7 - - - +
201P ALA* 1.3 61.3 + - - +
203P GLN* 3.2 12.6 + - - +
204P GLN* 2.9 41.6 + - - +
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Residues in contact with ALA 201 (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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151P PHE* 3.3 22.9 - - + -
154P LEU* 3.8 12.3 - - + -
155P GLU* 3.8 25.8 - - + +
158P MET* 3.8 5.5 - - - -
197P ILE 3.1 18.5 + - - +
198P ARG 3.7 0.4 - - - +
200P ALA* 1.3 75.5 - - - +
202P LEU* 1.3 64.3 + - - +
204P GLN* 3.0 2.3 + - - -
205P THR* 2.8 30.6 + - - +
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Residues in contact with LEU 202 (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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151P PHE* 3.4 32.3 - - + -
198P ARG* 3.1 48.3 + - + +
199P GLN* 4.1 18.2 - - - +
201P ALA* 1.3 78.4 - - - +
203P GLN* 1.3 63.1 - - - +
204P GLN 3.5 0.2 + - - -
205P THR* 3.8 11.7 + - - -
206P LYS* 3.9 12.1 - - - +
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Residues in contact with GLN 203 (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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108P HIS* 5.8 4.9 + - - -
199P GLN 3.3 14.5 + - - +
200P ALA* 3.2 16.4 + - - +
201P ALA 3.2 0.6 - - - -
202P LEU* 1.3 81.6 - - - +
204P GLN* 1.3 65.0 + - + +
206P LYS* 4.3 7.6 + - - +
207P GLU* 3.6 22.4 + - - +
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Residues in contact with GLN 204 (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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108P HIS* 2.7 50.7 - - + +
109P LEU 4.8 2.0 + - - +
154P LEU* 3.7 20.3 - - + +
158P MET* 3.0 32.5 - - - +
171P LEU 4.1 6.0 + - - +
172P VAL 4.7 3.0 - - - +
200P ALA* 2.9 23.9 + - - +
203P GLN* 1.3 82.1 - - + +
205P THR* 1.3 63.6 + - - +
206P LYS 3.2 3.1 - - - -
207P GLU* 3.2 19.6 + - - +
208P MET* 3.2 25.0 + - + +
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Residues in contact with THR 205 (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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150P VAL* 3.6 21.5 - - + +
151P PHE* 3.3 38.4 - - + +
154P LEU* 3.4 18.2 - - + -
201P ALA 2.8 23.1 + - - +
202P LEU* 3.8 9.9 + - - -
203P GLN 3.7 0.8 - - - -
204P GLN* 1.3 72.9 - - - +
206P LYS* 1.3 70.8 + - - +
208P MET* 3.3 17.0 - - - +
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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