Contacts of the strand formed by residues 185 - 198 (chain Y) in PDB entry 1IRA
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 LYS 185 (chain Y).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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181Y THR* 3.2 4.0 - - - -
182Y TYR 2.8 27.4 + - - +
183Y LEU 3.0 8.4 + - - +
184Y GLY* 1.3 79.8 - - - +
186Y GLN* 1.3 61.1 + - - +
187Y TYR* 3.4 32.5 - - + +
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Residues in contact with GLN 186 (chain Y).
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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179Y SER* 3.5 34.4 + - - -
180Y TYR 3.5 9.4 - - - +
181Y THR* 4.2 11.2 + - + +
184Y GLY 5.1 0.9 - - - +
185Y LYS* 1.3 77.1 - - - +
187Y TYR* 1.3 71.4 + - - +
188Y PRO* 4.5 1.9 - - - +
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Residues in contact with TYR 187 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17Y ASN 5.9 0.4 - - - -
19Y ILE* 3.7 28.0 - - + +
64Y VAL* 3.4 35.4 + - + +
65Y PRO* 4.4 26.2 - - + -
179Y SER* 3.3 4.2 - - - -
180Y TYR* 2.8 38.6 + - - +
182Y TYR* 3.7 34.9 + - + -
185Y LYS* 3.4 25.1 - - + +
186Y GLN* 1.3 79.1 - - - +
188Y PRO* 1.3 71.4 - - + +
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Residues in contact with PRO 188 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17Y ASN 3.8 13.5 - - - +
18Y GLU* 3.3 37.9 - - + +
19Y ILE 3.5 5.7 + - - -
178Y ALA 3.4 8.1 - - - +
179Y SER* 4.5 4.3 - - - +
186Y GLN 4.5 2.0 - - - +
187Y TYR* 1.3 90.1 - - + +
189Y ILE* 1.3 66.3 + - - +
190Y THR* 5.6 3.6 - - + -
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Residues in contact with ILE 189 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18Y GLU* 3.9 4.5 - - - -
19Y ILE* 3.8 15.0 - - + +
125Y MET* 3.8 27.4 - - + -
128Y PHE* 3.6 36.8 - - + -
136Y PRO* 5.0 0.7 - - + -
176Y CYS 3.6 0.6 - - - +
177Y HIS* 3.2 1.7 - - - +
178Y ALA* 2.8 41.9 + - + +
179Y SER 4.9 0.4 - - - -
180Y TYR* 3.7 22.2 - - + +
187Y TYR 4.4 2.0 - - - +
188Y PRO* 1.3 81.3 - - - +
190Y THR* 1.3 71.9 + - - +
191Y ARG* 3.8 26.5 - - - +
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Residues in contact with THR 190 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15Y SER* 3.9 13.9 + - - -
18Y GLU* 2.9 36.5 + - - +
96Y ASN* 5.6 0.7 + - - -
101Y CYS 5.4 6.4 + - - +
175Y THR* 5.4 4.3 - - - -
176Y CYS 3.1 7.6 - - - -
177Y HIS* 3.4 35.7 - - + +
188Y PRO* 5.6 3.1 - - + -
189Y ILE* 1.3 83.7 - - - +
191Y ARG* 1.3 79.8 + - - +
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Residues in contact with ARG 191 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14Y SER* 5.6 3.4 + - - -
18Y GLU* 5.7 0.6 + - - -
19Y ILE 5.2 2.4 + - - -
20Y ASP* 4.0 17.2 + - - -
108Y PHE* 4.5 17.5 - - + -
122Y CYS* 3.6 17.3 - - - -
123Y PRO* 2.7 38.0 + - + +
124Y TYR* 2.8 36.5 + - - +
125Y MET* 4.1 4.6 - - - -
127Y PHE* 4.8 1.4 - - - -
128Y PHE* 3.1 22.8 - - - -
174Y TYR 3.8 0.3 - - - +
175Y THR* 3.3 6.9 - - - -
176Y CYS* 3.1 36.5 + - - -
189Y ILE* 3.8 19.2 - - - +
190Y THR* 1.3 83.7 + - - +
192Y VAL* 1.3 61.3 + - - +
193Y ILE* 3.9 1.0 + - + -
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Residues in contact with VAL 192 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102Y TYR* 3.7 40.2 - - + -
103Y ASN 4.0 5.8 - - - +
106Y ALA* 3.3 38.6 + - + +
107Y ILE* 3.6 21.3 - - + +
108Y PHE* 3.1 30.8 + - - -
173Y ASN* 4.3 10.5 - - + -
174Y TYR 3.5 8.3 - - - +
175Y THR* 3.9 4.3 - - + -
191Y ARG* 1.3 72.8 - - - +
193Y ILE* 1.3 63.0 + - - +
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Residues in contact with ILE 193 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108Y PHE* 3.4 6.5 - - + +
110Y GLN* 3.2 41.1 - - + +
120Y LEU* 4.1 11.7 - - + -
121Y VAL 3.2 28.0 - - - +
122Y CYS* 4.0 0.9 - - - -
123Y PRO* 3.8 18.6 - - + -
140Y TRP* 3.8 26.7 - - + -
173Y ASN* 3.4 3.6 - - - -
174Y TYR* 2.7 46.7 + - + +
176Y CYS* 4.4 2.9 - - - -
191Y ARG 4.5 3.6 - - - +
192Y VAL* 1.3 79.2 - - - +
194Y GLU* 1.3 63.9 + - - +
195Y PHE 3.6 1.2 + - - -
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Residues in contact with GLU 194 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107Y ILE* 3.4 20.2 - - + +
108Y PHE 2.9 10.4 + - - +
109Y LYS* 3.2 39.4 + - - +
110Y GLN 3.0 26.2 + - - +
172Y GLY 3.9 0.4 - - - -
173Y ASN* 3.1 20.2 - - - +
193Y ILE* 1.3 73.0 - - - +
195Y PHE* 1.3 59.2 + - - +
196Y ILE* 3.6 15.2 + - + +
401Y NAG 2.9 47.8 + - + +
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Residues in contact with PHE 195 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110Y GLN* 3.3 9.4 - - + -
111Y LYS 4.4 0.9 - - - -
112Y LEU* 3.6 47.6 - - + -
120Y LEU* 3.6 31.4 - - + -
163Y VAL* 5.0 5.6 - - + -
166Y VAL* 3.9 19.5 - - + -
170Y HIS* 3.2 43.5 - + + +
171Y ARG* 3.7 8.0 - - - +
172Y GLY 3.0 30.6 + - - +
174Y TYR* 3.8 15.7 - + + -
193Y ILE 3.6 1.8 + - - -
194Y GLU* 1.3 70.5 - - - +
196Y ILE* 1.3 65.6 + - - +
197Y THR* 4.1 12.3 - - + -
401Y NAG 3.8 6.6 - - - +
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Residues in contact with ILE 196 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109Y LYS* 4.1 31.6 - - + +
110Y GLN 2.9 10.8 + - - +
111Y LYS* 3.1 32.6 - - + +
112Y LEU 3.2 6.4 + - - -
171Y ARG* 4.7 13.0 - - - +
194Y GLU* 4.2 22.4 - - + +
195Y PHE* 1.3 80.6 - - - +
197Y THR* 1.3 72.6 + - - +
198Y LEU* 4.5 11.0 - - + -
401Y NAG 5.4 1.8 - - + -
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Residues in contact with THR 197 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112Y LEU 3.5 3.6 - - - -
114Y VAL* 3.8 14.8 - - - +
166Y VAL* 3.7 20.0 - - + -
167Y ALA 3.4 25.1 - - - +
168Y GLU* 3.9 7.9 - - - +
171Y ARG* 3.1 33.5 + - + +
195Y PHE* 4.1 11.2 - - + -
196Y ILE* 1.3 82.2 - - - +
198Y LEU* 1.3 63.4 + - - +
199Y GLU* 4.0 4.2 + - - +
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Residues in contact with LEU 198 (chain Y).
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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14X ARG* 5.6 3.1 - - - +
16X TRP* 3.3 38.6 - - + -
149X GLN* 3.6 27.1 - - - +
111Y LYS* 4.0 26.5 - - + -
112Y LEU 2.9 16.9 + - - +
113Y PRO* 3.3 6.4 - - + +
114Y VAL* 2.9 28.8 + - - +
196Y ILE* 4.5 9.2 - - + -
197Y THR* 1.3 77.3 - - - +
199Y GLU* 1.3 64.2 + - - +
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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