Contacts of the helix formed by residues 191 - 204 (chain I) in PDB entry 5OA3
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 GLU 191 (chain I).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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66I SER 4.5 0.3 - - - +
67I TRP* 3.5 15.7 - - - -
68I GLY* 2.5 35.4 + - - -
69I SER* 2.2 36.9 + - - +
162I LEU* 4.2 16.1 - - + +
188I TYR* 5.9 1.1 - - + -
189I VAL* 3.5 14.8 + - + +
190I LEU* 1.3 79.0 - - - +
192I GLY* 1.3 64.7 + - - +
193I LYS 3.4 0.9 + - - -
194I GLU* 3.8 8.6 + - - +
195I LEU* 3.6 4.9 - - - +
17L PHE* 5.3 2.2 - - + -
19L ASN* 2.6 45.3 + - + +
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Residues in contact with GLY 192 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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159I SER* 5.2 11.3 + - - -
161I LEU* 4.9 4.1 - - - +
162I LEU* 4.9 3.8 - - - +
191I GLU* 1.3 71.9 - - - +
193I LYS* 1.3 59.0 + - - -
195I LEU* 3.0 11.8 + - - +
196I GLU* 2.9 32.6 + - - +
19L ASN* 3.8 6.3 - - - -
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Residues in contact with LYS 193 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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191I GLU 3.4 2.2 + - - -
192I GLY* 1.3 71.3 - - - -
194I GLU* 1.3 58.1 + - - +
196I GLU* 3.0 25.5 - - - +
197I PHE* 2.9 26.6 + - - +
10L TYR* 4.2 9.8 - - + +
18L GLN* 3.8 20.0 - - - +
19L ASN* 3.8 4.9 + - - +
31L GLU* 4.1 30.6 + - - +
33L LEU* 4.3 29.2 - - + +
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Residues in contact with GLU 194 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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188I TYR* 3.3 22.2 + - - -
190I LEU* 3.3 23.4 - - + +
191I GLU 3.8 12.5 + - - +
193I LYS* 1.3 71.8 - - - +
195I LEU* 1.3 64.6 + - - +
197I PHE* 3.1 2.0 + - - -
198I TYR* 2.9 41.6 + - + -
10L TYR* 4.0 33.9 - - + -
12L LYS* 3.5 26.0 - - - +
18L GLN* 3.8 19.6 + - - +
19L ASN* 4.1 12.0 + - - +
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Residues in contact with LEU 195 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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159I SER* 6.0 0.9 - - - -
161I LEU* 4.1 20.9 - - + -
162I LEU* 3.8 26.0 - - + +
165I GLN* 3.9 17.3 - - - +
172I LEU* 4.0 9.2 - - + -
190I LEU* 3.2 43.5 - - + +
191I GLU 3.6 11.9 + - - +
192I GLY 3.0 16.7 + - - +
194I GLU* 1.3 80.8 - - - +
196I GLU* 1.3 55.9 + - - +
198I TYR* 3.9 0.9 - - - +
199I LEU* 2.9 51.5 + - + +
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Residues in contact with GLU 196 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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161I LEU* 4.2 15.0 - - + +
192I GLY 2.9 10.3 + - - +
193I LYS* 3.0 38.9 + - - +
195I LEU* 1.3 76.0 - - - +
197I PHE* 1.3 60.8 + - + +
199I LEU* 3.5 10.5 - - - +
200I ARG* 2.9 29.8 + - - +
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Residues in contact with PHE 197 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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193I LYS 2.9 13.9 + - - +
194I GLU* 3.1 8.9 + - - +
196I GLU* 1.3 80.4 - - + +
198I TYR* 1.3 76.4 + + - +
200I ARG* 3.1 32.4 + - - +
201I LYS* 2.9 55.8 + - + +
5L GLN* 4.3 20.4 - - + -
7L GLU 3.9 10.1 - - - -
8L ARG 3.9 8.7 - - - -
10L TYR* 3.5 52.9 - + + -
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Residues in contact with TYR 198 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83I TYR* 3.8 27.8 - + - -
85I ALA* 5.9 0.9 - - + -
99I ASN* 4.3 15.4 + - - -
101I ILE* 3.3 36.8 - - + -
172I LEU* 5.7 1.6 - - + -
174I CYS* 6.4 2.0 - - + -
188I TYR* 6.1 0.9 - - - -
190I LEU* 4.3 17.7 - - + -
194I GLU* 2.9 34.9 + - + +
195I LEU 4.2 2.0 - - - +
197I PHE* 1.3 86.8 - + - +
199I LEU* 1.3 60.0 + - - +
201I LYS* 3.4 5.7 - - + +
202I ILE* 2.9 41.3 + - + +
8L ARG 4.2 2.2 - - - -
9L ALA* 3.9 4.2 - - - +
10L TYR* 2.9 43.8 + - + +
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Residues in contact with LEU 199 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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161I LEU* 4.1 27.6 - - + -
165I GLN* 4.4 9.2 - - - +
172I LEU* 4.1 19.7 - - + +
195I LEU* 2.9 49.3 + - + +
196I GLU* 3.5 5.4 - - - +
198I TYR* 1.3 76.1 - - - +
200I ARG* 1.3 56.7 + - - +
202I ILE* 3.3 7.2 + - + +
203I LYS* 2.9 31.4 + - - +
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Residues in contact with ARG 200 (chain I).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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196I GLU 2.9 14.7 + - - +
197I PHE* 3.2 44.4 - - - +
199I LEU* 1.3 76.4 - - - +
201I LYS* 1.3 66.5 + - + +
203I LYS* 3.7 15.1 - - + +
204I ALA* 2.9 28.0 + - + +
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Residues in contact with LYS 201 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83I TYR* 4.8 18.8 - - + +
197I PHE* 2.9 51.8 + - + +
198I TYR* 3.0 18.8 + - + +
200I ARG* 1.3 87.8 - - + +
202I ILE* 1.3 61.7 + - + +
204I ALA* 3.1 13.0 - - + +
205I ARG* 3.1 20.8 + - - +
6L THR 5.2 4.8 + - - -
7L GLU 4.4 10.5 + - - -
8L ARG* 4.5 16.4 - - - +
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Residues in contact with ILE 202 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82I VAL* 3.9 36.1 - - + +
83I TYR* 4.1 25.6 - - + -
101I ILE* 5.0 4.0 - - + -
172I LEU* 4.3 20.2 - - + -
198I TYR* 2.9 26.6 + - + +
199I LEU* 4.0 5.4 - - + +
201I LYS* 1.3 74.1 - - + +
203I LYS* 1.3 63.6 + - - +
204I ALA 3.1 0.7 - - - -
205I ARG* 2.9 31.5 + - + +
206I LYS* 3.4 24.2 - - - +
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Residues in contact with LYS 203 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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199I LEU 2.9 18.6 + - - +
200I ARG* 3.7 14.7 - - + +
202I ILE* 1.3 76.0 - - - +
204I ALA* 1.3 57.4 + - - +
205I ARG 3.1 0.2 - - - -
206I LYS* 3.1 38.6 + - + +
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Residues in contact with ALA 204 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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200I ARG* 2.9 17.0 + - + +
201I LYS* 3.1 22.9 - - + +
202I ILE 3.1 0.2 - - - -
203I LYS* 1.3 76.0 - - - +
205I ARG* 1.3 58.3 + - - +
206I LYS 3.1 7.1 + - - -
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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