Contacts of the helix formed by residues 1236 - 1249 (chain A) in PDB entry 3B13
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 ASN1236 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1201A MET* 4.8 5.9 - - - +
1231A HIS* 2.9 29.1 + - - +
1232A LEU* 4.9 0.7 - - - -
1234A CYS* 3.5 27.0 - - - +
1235A ASP* 1.3 75.4 - - - +
1237A TYR* 1.3 64.5 + - - +
1238A THR 3.3 1.8 - - - -
1239A GLU* 3.1 32.2 - - + +
1240A ALA* 3.1 21.7 + - - +
1480A ARG* 3.9 30.6 + - - +
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Residues in contact with TYR1237 (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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1232A LEU* 3.8 26.2 + - + -
1235A ASP* 3.2 50.9 + - + -
1236A ASN* 1.3 70.4 - - - +
1238A THR* 1.3 61.4 + - - +
1239A GLU* 4.7 0.2 + - - -
1240A ALA* 3.4 3.7 + - - +
1241A ALA* 2.9 23.4 + - - +
1287A TYR* 3.3 44.1 - + - +
1290A LYS* 3.7 52.1 + - + +
1291A GLY* 4.1 6.9 - - - +
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Residues in contact with THR1238 (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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1236A ASN 3.3 0.2 - - - -
1237A TYR* 1.3 77.7 - - - +
1239A GLU* 1.3 78.3 + - - +
1241A ALA* 3.1 3.3 + - - +
1242A TYR* 2.9 54.7 + - + -
1287A TYR 4.5 0.9 + - - -
1288A PHE* 4.1 9.4 - - + -
1291A GLY* 3.8 15.4 + - - -
1293A MET* 3.6 25.4 - - + +
1364A ARG* 4.3 6.2 + - - +
1476A PRO* 3.5 22.7 - - + -
1480A ARG* 5.8 0.2 + - - -
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Residues in contact with GLU1239 (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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1231A HIS* 3.5 22.4 - - + +
1236A ASN* 3.1 35.6 - - + +
1238A THR* 1.3 90.0 + - - +
1240A ALA* 1.3 56.7 + - - +
1242A TYR 3.6 0.5 + - - -
1243A THR* 2.8 32.4 + - - -
1364A ARG* 4.4 1.0 + - - -
1476A PRO* 4.3 10.7 - - - +
1477A GLY 3.2 26.4 - - - +
1478A ILE* 3.9 5.0 - - - +
1479A LEU 4.0 5.9 - - - +
1480A ARG* 3.3 50.4 + - + +
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Residues in contact with ALA1240 (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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1228A ARG* 4.0 7.7 - - + +
1231A HIS* 3.9 14.1 - - + +
1232A LEU* 3.6 26.0 - - + -
1236A ASN 3.1 19.1 + - - +
1237A TYR 3.4 5.8 - - - +
1239A GLU* 1.3 75.5 - - - +
1241A ALA* 1.3 65.1 + - - +
1243A THR* 3.2 5.4 + - - -
1244A LEU* 3.0 27.4 + - - +
1287A TYR* 3.6 11.9 - - + -
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Residues in contact with ALA1241 (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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1237A TYR 2.9 13.0 + - - +
1238A THR 3.1 2.9 + - - +
1240A ALA* 1.3 74.8 - - - +
1242A TYR* 1.3 65.6 + - - +
1243A THR 3.0 0.7 + - - -
1244A LEU* 3.0 4.5 + - - +
1245A LEU* 3.0 23.0 + - - +
1284A ILE* 3.9 13.1 - - + +
1287A TYR* 3.6 19.9 - - + -
1288A PHE* 3.3 41.5 - - + -
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Residues in contact with TYR1242 (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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1238A THR* 2.9 49.8 + - + +
1241A ALA* 1.3 75.8 - - - +
1243A THR* 1.3 63.7 + - - +
1245A LEU* 3.5 25.3 + - + +
1246A LEU* 3.6 5.9 + - - +
1288A PHE* 3.5 17.9 - + - -
1293A MET* 4.4 0.6 - - + +
1296A GLU* 2.8 31.5 + - - +
1438A TYR* 3.4 23.6 - - - -
1474A LYS* 5.5 5.9 - - - -
1476A PRO* 3.7 20.5 + - + +
1477A GLY* 3.6 36.3 - - - +
1478A ILE* 3.6 13.6 - - + +
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Residues in contact with THR1243 (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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1224A LEU* 3.4 40.4 - - + +
1227A LEU* 3.7 16.6 - - + +
1228A ARG* 4.1 13.0 - - + +
1231A HIS* 3.5 14.2 - - - -
1239A GLU 2.8 20.2 + - - -
1240A ALA* 3.3 11.4 - - - -
1241A ALA 3.0 1.0 + - - -
1242A TYR* 1.3 77.1 - - - +
1244A LEU* 1.3 58.8 + - + +
1246A LEU* 2.8 31.7 + - - +
1247A HIS 3.9 0.7 + - - -
1478A ILE* 3.8 12.2 - - - +
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Residues in contact with LEU1244 (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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1224A LEU* 5.3 2.7 - - + +
1225A TYR* 3.2 43.3 - - + +
1228A ARG* 3.8 24.2 - - + +
1240A ALA 3.0 17.0 + - - +
1243A THR* 1.3 79.4 - - + +
1245A LEU* 1.3 56.6 + - - +
1246A LEU 3.0 0.2 - - - -
1247A HIS* 2.8 27.0 + - + +
1248A THR* 3.0 11.8 + - - +
1280A LEU* 4.6 12.3 - - + -
1283A THR* 3.7 30.7 - - + -
1284A ILE* 3.8 22.0 - - + -
1287A TYR* 3.9 10.8 - - + -
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Residues in contact with LEU1245 (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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1241A ALA 3.0 12.7 + - - +
1242A TYR* 3.5 23.3 - - + +
1243A THR 3.1 0.4 + - - -
1244A LEU* 1.3 76.0 - - - +
1246A LEU* 1.3 58.0 + - + +
1247A HIS 3.2 0.2 - - - -
1248A THR* 3.3 20.6 + - - +
1249A TRP* 3.0 29.6 + - - +
1281A TYR* 4.5 3.8 - - + +
1284A ILE* 4.0 17.4 - - + +
1288A PHE* 4.2 27.6 - - + -
1296A GLU* 5.9 2.5 - - - +
1300A LEU* 4.2 25.6 - - + -
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Residues in contact with LEU1246 (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 LEU* 4.1 13.5 - - + -
1220A TYR* 3.6 22.7 + - - +
1224A LEU* 3.5 29.4 - - + -
1242A TYR 3.9 8.1 - - - +
1243A THR* 2.8 17.4 + - + +
1245A LEU* 1.3 79.5 - - - +
1247A HIS* 1.3 61.2 - - - +
1249A TRP* 3.4 18.4 - - + +
1250A LEU* 3.9 11.6 - - - +
1478A ILE* 4.0 25.1 - - + -
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Residues in contact with HIS1247 (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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1221A ILE* 4.0 18.2 - - + +
1224A LEU* 3.4 20.3 - - + +
1225A TYR* 2.6 40.8 + + + +
1244A LEU* 2.8 13.1 + - - +
1246A LEU* 1.3 75.9 - - - +
1248A THR* 1.3 60.6 + - - +
1249A TRP 3.0 1.8 - - - -
1250A LEU* 2.8 27.5 + - + +
1251A LEU* 3.8 11.6 + - + +
1262A VAL* 2.9 27.4 + - + -
1264A GLN* 4.5 10.5 - - + -
1267A GLN* 5.4 0.9 - - - -
1276A LEU* 4.1 15.6 - - + +
1280A LEU* 3.4 16.8 - - + +
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Residues in contact with THR1248 (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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1244A LEU 3.0 3.4 + - - +
1245A LEU* 3.3 25.1 + - - +
1247A HIS* 1.3 75.2 - - - +
1249A TRP* 1.3 63.2 + - - +
1250A LEU 3.0 1.3 + - - -
1251A LEU* 3.1 28.8 + - - +
1277A LYS* 3.8 15.1 + - + +
1280A LEU* 3.5 38.1 - - + -
1281A TYR* 3.7 21.7 + - + -
1284A ILE* 3.6 20.0 - - + -
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Residues in contact with TRP1249 (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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1245A LEU 3.0 18.3 + - - +
1246A LEU* 3.4 14.1 - - + +
1248A THR* 1.3 80.0 + - - +
1250A LEU* 1.3 73.5 + - + +
1251A LEU 3.6 4.0 + - - +
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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