Contacts of the strand formed by residues 1237 - 1242 (chain A) in PDB entry 6BM4
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 ILE1237 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1165A GLU* 4.6 10.1 - - + +
1166A ASP* 3.5 22.7 - - - +
1169A ILE* 5.1 7.9 - - + -
1194A ARG* 3.3 56.8 - - + +
1195A LEU 3.3 4.7 - - - +
1196A GLU* 5.6 4.0 - - + -
1209A MET* 3.6 2.2 - - - +
1228A TRP* 3.3 6.6 - - - +
1229A SER* 3.2 30.0 + - - +
1235A LYS* 3.1 38.4 + - + +
1236A LEU* 1.3 75.7 - - - +
1238A ILE* 1.3 71.1 + - - +
1239A ARG* 4.4 2.9 - - + -
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Residues in contact with ILE1238 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1193A LEU 3.4 1.2 - - - +
1194A ARG* 3.2 7.1 - - - +
1195A LEU* 2.9 52.8 + - + +
1197A LEU* 4.1 15.0 - - + -
1209A MET* 3.8 13.5 - - + -
1212A VAL* 3.6 32.5 - - + -
1213A GLY* 4.9 4.9 - - - +
1216A ILE* 4.1 13.5 - - + -
1226A VAL* 3.9 11.2 - - + -
1227A ILE 3.5 10.8 - - - +
1228A TRP* 4.2 5.8 - - + -
1237A ILE* 1.3 79.9 - - - +
1239A ARG* 1.3 66.4 + - - +
1240A CYS* 3.8 22.0 - - - -
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Residues in contact with ARG1239 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1155A ASP* 2.9 28.3 + - - -
1158A PRO 5.1 1.6 + - - -
1161A THR* 3.0 16.7 + - - +
1166A ASP* 3.2 37.4 + - - +
1169A ILE* 4.3 20.0 - - + -
1170A ILE* 4.0 7.8 - - - +
1192A LEU* 3.3 26.5 - - + +
1193A LEU 3.6 2.9 - - - -
1194A ARG* 5.0 2.7 - - + -
1225A PHE 3.6 1.1 - - - +
1226A VAL* 3.3 5.4 - - - -
1227A ILE* 2.9 61.7 + - + +
1237A ILE* 4.5 7.4 - - + +
1238A ILE* 1.3 76.4 - - - +
1240A CYS* 1.3 64.2 + - - +
1241A ARG* 3.1 22.9 - - + +
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Residues in contact with CYS1240 (chain A).
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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1191A TRP 4.0 0.7 - - - +
1192A LEU* 3.8 2.6 - - - +
1193A LEU* 2.9 51.3 + - + +
1195A LEU* 5.4 0.9 - - - -
1216A ILE* 4.7 1.8 - - - -
1224A LEU* 3.8 23.1 - - + -
1225A PHE 3.3 5.2 - - - +
1226A VAL* 4.1 15.0 - - - -
1238A ILE* 3.8 21.1 - - - -
1239A ARG* 1.3 80.9 - - - +
1241A ARG* 1.3 66.9 + - - +
1260A LEU* 5.1 2.0 - - - +
1267A MET* 4.6 19.3 - - - -
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Residues in contact with ARG1241 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1155A ASP* 2.8 55.1 + - - +
1156A PRO 4.5 2.8 + - - -
1158A PRO* 4.0 21.6 + - - +
1188A GLN* 3.4 24.7 + - + +
1189A SER 3.0 32.6 + - - +
1190A PRO* 3.6 5.5 + - - +
1191A TRP 4.0 8.8 + - - +
1192A LEU* 4.1 8.9 - - + +
1224A LEU* 3.2 10.1 - - - +
1225A PHE* 2.9 47.6 + - + +
1227A ILE* 5.7 1.4 - - - +
1239A ARG* 3.1 28.1 - - - +
1240A CYS* 1.3 81.2 - - - +
1242A VAL* 1.3 62.6 + - - +
1243A VAL* 6.0 0.2 - - + -
1260A LEU* 5.9 0.2 - - - -
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Residues in contact with VAL1242 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1188A GLN* 3.7 1.9 - - - -
1189A SER* 3.2 31.8 + - - -
1191A TRP* 4.7 2.0 + - + +
1223A ASP* 4.0 13.5 - - + +
1224A LEU* 4.5 2.9 - - + -
1241A ARG* 1.3 73.8 - - - +
1243A VAL* 1.3 69.8 + - - +
1256A GLU* 4.0 24.7 - - + +
1260A LEU* 3.7 31.9 - - + -
1263A ILE* 3.9 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