Contacts of the strand formed by residues 1239 - 1245 (chain C) in PDB entry 1I7M
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 TYR1239 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1071C PHE* 3.7 37.7 - + + -
1076C ARG* 3.8 15.9 - - - -
1078C ILE* 3.5 25.8 - - + +
1176C THR* 3.8 15.3 + - - +
1232C GLY 3.3 5.4 - - - +
1238C THR* 1.3 72.9 - - - +
1240C TRP* 1.3 62.8 + - - +
1241C THR* 5.2 0.7 - - - -
1256C GLU* 2.8 43.8 + - + +
1257C THR* 2.6 37.2 + - - -
1258C ASN* 2.9 52.8 + - + -
1015D GLU* 4.0 3.7 + - - -
1060D GLN* 3.4 20.0 - - - +
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Residues in contact with TRP1240 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1071C PHE* 4.2 0.9 - - - -
1209C ILE* 3.2 28.3 - - + -
1210C ARG 3.9 5.2 - - - -
1212C LEU* 4.0 11.2 - - + -
1213C ILE* 3.4 48.4 - - + +
1216C SER* 3.0 30.0 + - - -
1218C ILE* 4.0 8.7 - - + -
1230C MSE 3.4 36.2 - - + +
1231C ASN 3.4 0.2 - - - -
1232C GLY* 2.5 51.6 + - - +
1233C MSE 4.1 1.8 - - - -
1234C LYS 5.3 0.2 - - - -
1238C THR* 4.8 4.5 - - + -
1239C TYR* 1.3 82.3 - - - +
1241C THR* 1.3 62.1 + - - +
1242C ILE* 4.1 12.1 - - + -
1255C PHE* 3.7 17.9 - + + -
1256C GLU 3.1 15.7 - - - +
1257C THR* 3.5 9.9 - - - +
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Residues in contact with THR1241 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1069C SER* 3.0 9.9 - - - +
1071C PHE* 2.9 27.5 - - - -
1080C LYS* 5.4 5.6 + - + -
1230C MSE 2.9 20.4 - - - +
1231C ASN* 2.4 17.8 + - - -
1239C TYR* 4.8 1.3 - - - -
1240C TRP* 1.3 71.6 - - - +
1242C ILE* 1.3 63.6 + - - +
1243C HIS* 2.9 37.9 - - + +
1254C SER 4.0 0.7 - - - +
1255C PHE* 3.6 2.6 - - - -
1256C GLU* 3.0 38.4 + - - +
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Residues in contact with ILE1242 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1209C ILE* 3.6 33.9 - - + -
1212C LEU* 3.9 14.8 - - + -
1228C TYR* 4.0 3.4 - - + +
1229C SER* 3.7 1.4 - - - -
1230C MSE 3.0 39.9 + - + +
1240C TRP* 4.1 7.2 - - + -
1241C THR* 1.3 74.2 - - - +
1243C HIS* 1.3 69.0 + - - +
1244C ILE* 4.0 21.8 - - + -
1253C VAL* 4.4 1.3 - - + -
1254C SER 3.1 11.4 - - - +
1255C PHE* 3.5 34.5 - - + -
1275C PHE* 4.0 20.0 - - + -
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Residues in contact with HIS1243 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1068C PYR 3.5 25.8 - - + -
1069C SER* 2.7 34.3 + - - -
1080C LYS* 4.7 6.5 - - + -
1228C TYR 3.5 2.0 - - - -
1229C SER* 2.7 36.3 + - - -
1230C MSE 4.5 0.7 - - - -
1241C THR* 2.9 23.5 - - + +
1242C ILE* 1.3 71.5 + - - +
1244C ILE* 1.3 63.2 + - - +
1245C THR* 5.6 0.2 - - - -
1252C TYR* 3.7 3.7 - - + +
1253C VAL* 3.2 5.0 - - - -
1254C SER* 3.0 33.5 + - - -
1009D GLY 5.8 0.9 - - - +
1011D GLU* 3.5 25.4 - - - +
1064D VAL* 5.5 0.2 - - + -
1375D CG 3.7 13.9 + + + -
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Residues in contact with ILE1244 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1189C MSE 3.7 17.9 - - - -
1192C PHE* 3.3 55.2 - - + -
1209C ILE* 4.1 4.0 - - + -
1227C GLY* 3.5 4.7 - - - -
1228C TYR* 2.9 45.4 + - + +
1242C ILE* 4.0 8.5 - - + -
1243C HIS* 1.3 78.5 - - - +
1245C THR* 1.3 65.6 + - - +
1246C PRO* 3.7 8.1 - - + -
1252C TYR 3.5 2.5 - - - -
1253C VAL* 3.7 22.2 - - + -
1275C PHE* 3.7 13.2 - - + -
1375D CG 3.4 12.3 - - - -
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Residues in contact with THR1245 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1189C MSE 3.0 4.6 - - - +
1243C HIS 5.6 0.2 - - - -
1244C ILE* 1.3 72.6 + - - +
1246C PRO* 1.3 61.0 - - - +
1247C GLU* 3.7 0.9 - - - +
1250C PHE* 3.6 37.5 - - + +
1251C SER* 3.1 6.8 - - - -
1252C TYR* 2.8 40.7 + - - -
1007D PHE* 3.6 21.7 - - + +
1009D GLY* 3.5 19.9 - - - +
1375D CG 3.4 19.7 - - - +
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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