Contacts of the helix formed by residues 1257 - 1267 (chain A) in PDB entry 3F2B
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 PRO1257 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1219A TYR* 3.3 19.7 - - - +
1223A ARG* 5.3 4.3 - - - +
1255A ASP 3.2 8.3 - - - +
1256A VAL* 1.3 94.1 - - + +
1258A GLU* 1.3 65.6 + - - +
1259A TRP* 3.2 37.2 + - + +
1260A TYR* 3.2 13.1 + - + +
1261A ILE* 3.3 11.9 + - - +
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Residues in contact with GLU1258 (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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1252A ARG* 2.6 53.7 + - - +
1256A VAL 5.1 0.7 - - - +
1257A PRO* 1.3 72.8 - - - +
1259A TRP* 1.3 59.7 + - - +
1261A ILE* 4.0 10.0 - - - +
1262A ASP* 3.2 24.8 + - + +
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Residues in contact with TRP1259 (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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1198A LEU* 3.8 38.6 - - + +
1203A THR* 3.8 28.3 + - - +
1204A CYS* 3.7 28.9 - - + -
1208A GLU* 4.2 11.2 - - + -
1209A VAL* 5.5 1.6 - - - -
1210A ILE* 5.7 2.7 - - + -
1219A TYR* 5.9 1.1 - + - -
1257A PRO* 3.5 27.7 - - + +
1258A GLU* 1.3 76.8 - - - +
1260A TYR* 1.3 107.6 + + + +
1262A ASP* 3.8 6.4 - - - +
1263A SER* 2.9 32.5 + - - -
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Residues in contact with TYR1260 (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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1208A GLU 5.1 4.7 - - - -
1210A ILE* 3.6 22.7 - - + +
1215A ASP 4.1 1.7 + - - -
1216A ILE* 3.2 39.3 + - + +
1219A TYR* 3.5 37.4 - + + -
1220A LEU* 4.8 2.2 - - + -
1251A MET* 4.1 7.4 - - + -
1256A VAL* 3.8 18.6 - - + -
1257A PRO* 3.2 15.5 + - + +
1259A TRP* 1.3 117.0 - + + +
1261A ILE* 1.3 62.2 + - - +
1263A SER* 3.2 3.8 + - - -
1264A CYS* 3.0 40.1 + - - -
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Residues in contact with ILE1261 (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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1243A LEU* 3.4 21.2 - - + +
1248A GLU* 4.3 17.5 - - + +
1251A MET* 3.9 35.9 - - + -
1252A ARG* 3.8 42.6 - - + +
1256A VAL* 4.1 11.9 - - + +
1257A PRO 3.3 14.0 + - - +
1258A GLU* 4.0 14.1 - - - +
1260A TYR* 1.3 77.7 - - - +
1262A ASP* 1.3 62.6 + - - +
1264A CYS 3.3 1.7 + - - -
1265A LYS* 3.2 29.0 + - + +
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Residues in contact with ASP1262 (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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1258A GLU* 3.2 18.0 + - + +
1259A TRP* 3.8 6.6 - - - +
1261A ILE* 1.3 80.7 - - - +
1263A SER* 1.3 62.2 + - - +
1265A LYS* 3.2 26.5 + - - +
1266A LYS* 3.3 43.4 + - - +
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Residues in contact with SER1263 (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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1194A ASN* 2.9 34.3 + - - +
1198A LEU* 4.1 14.5 - - - +
1210A ILE* 3.8 18.9 + - - +
1259A TRP* 2.9 20.6 + - - -
1260A TYR* 3.2 8.7 + - - -
1262A ASP* 1.3 76.6 + - - +
1264A CYS* 1.3 64.6 + - - +
1266A LYS* 3.1 11.5 + - - -
1267A ILE* 3.3 16.1 - - - +
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Residues in contact with CYS1264 (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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1210A ILE* 3.9 9.9 - - - -
1216A ILE* 4.5 9.0 - - - -
1233A ILE* 5.5 0.2 - - - -
1237A VAL* 3.8 41.3 - - + +
1242A GLY* 4.3 5.5 - - - -
1243A LEU* 3.5 16.6 - - + -
1251A MET* 4.2 8.5 - - - -
1260A TYR* 3.0 42.2 + - - -
1261A ILE 3.5 9.6 - - - +
1263A SER* 1.3 75.2 - - - +
1265A LYS* 1.3 62.6 + - - +
1266A LYS 3.2 0.5 + - - -
1267A ILE* 3.7 11.7 + - - +
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Residues in contact with LYS1265 (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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1242A GLY* 4.4 13.0 - - - -
1243A LEU* 3.7 28.9 + - + +
1248A GLU* 2.7 29.2 + - - +
1261A ILE* 3.2 21.3 + - + +
1262A ASP* 3.2 20.2 + - - +
1263A SER 3.2 1.0 - - - -
1264A CYS* 1.3 77.2 - - - +
1266A LYS* 1.3 63.8 + - + +
1267A ILE 4.7 1.2 - - - +
1268A LYS* 4.8 3.8 + - - -
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Residues in contact with LYS1266 (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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1189A ASP* 3.4 23.6 - - + +
1193A GLY 2.9 28.1 + - - +
1194A ASN* 4.0 17.2 + - + +
1197A GLU* 4.2 8.3 + - - -
1262A ASP* 3.3 37.4 + - - +
1263A SER* 3.1 6.4 + - - +
1264A CYS 3.1 1.4 - - - -
1265A LYS* 1.3 81.1 - - + +
1267A ILE* 1.3 66.5 + - - +
1268A LYS* 3.0 27.3 + - - +
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Residues in contact with ILE1267 (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 THR 4.2 0.4 - - - -
1189A ASP 4.0 7.4 - - - +
1190A VAL* 3.8 12.6 - - + -
1194A ASN* 3.7 13.7 - - - +
1210A ILE* 3.8 39.0 - - + +
1237A VAL* 3.4 27.2 - - + +
1240A GLY* 3.2 18.2 - - - -
1242A GLY 5.2 0.9 + - - -
1263A SER 3.3 18.6 + - - +
1264A CYS* 3.7 4.8 + - - +
1265A LYS 3.6 2.4 - - - +
1266A LYS* 1.3 73.1 - - - +
1268A LYS* 1.3 59.2 + - - +
1269A TYR 3.4 29.2 - - - +
1270A MET* 3.8 18.6 - - + -
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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