Contacts of the helix formed by residues 1427 - 1437 (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 PRO1427 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1333A MET* 5.6 1.3 - - + -
1425A PRO 3.6 7.4 - - - +
1426A VAL* 1.3 97.7 - - + +
1428A ASP* 1.3 67.8 + - - +
1429A GLN* 4.4 5.4 - - + +
1430A ILE* 2.8 40.0 + - + -
1431A ILE* 3.2 9.5 + - - +
1312C ILE 5.3 0.7 - - - +
1313C PHE* 3.6 19.1 - - + +
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Residues in contact with ASP1428 (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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1426A VAL 4.8 2.9 - - - +
1427A PRO* 1.3 72.6 - - - +
1429A GLN* 1.3 64.9 + - - +
1430A ILE 3.0 0.2 + - - -
1431A ILE* 4.1 9.8 - - - +
1432A ASN* 2.9 47.3 + - - +
1511A MET* 3.6 30.4 - - + +
1514A ASN* 3.5 31.1 + - + +
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Residues in contact with GLN1429 (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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1332A ILE* 3.5 20.0 + - - +
1333A MET* 3.1 51.3 + - + +
1335A ILE 4.3 11.3 + - - -
1336A LEU* 5.5 2.6 - - - +
1337A ARG* 5.2 1.4 + - - +
1427A PRO* 3.0 3.6 + - + +
1428A ASP* 1.3 79.4 - - - +
1430A ILE* 1.3 60.3 + - - +
1432A ASN* 4.6 8.2 + - - +
1433A PHE* 4.8 7.8 + - - +
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Residues in contact with ILE1430 (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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1295A GLU* 5.1 3.5 - - - +
1332A ILE* 4.8 5.4 - - + +
1333A MET* 3.2 33.9 - - + -
1421A PHE* 4.5 12.8 - - + -
1426A VAL* 3.5 18.6 - - + -
1427A PRO* 2.8 38.0 + - + +
1429A GLN* 1.3 80.8 - - - +
1431A ILE* 1.3 62.4 + - - +
1432A ASN 3.6 0.2 - - - -
1433A PHE* 4.0 8.3 + - - +
1434A TYR* 3.7 17.3 - - + -
1313C PHE* 3.8 14.6 - - + +
1315C TYR* 3.5 39.0 - - + +
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Residues in contact with ILE1431 (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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1415A LEU* 4.1 24.5 - - + -
1421A PHE* 3.6 39.5 - - + -
1426A VAL* 3.9 21.5 - - + +
1427A PRO 3.2 13.0 + - - +
1428A ASP* 3.9 12.1 - - - +
1430A ILE* 1.3 77.2 - - - +
1432A ASN* 1.3 73.1 + - - +
1433A PHE 3.2 3.1 - - - -
1434A TYR* 3.0 15.7 + - - +
1435A LYS* 3.1 14.4 + - + +
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Residues in contact with ASN1432 (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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1428A ASP* 2.9 37.6 + - - +
1429A GLN* 4.5 8.9 + - - +
1431A ILE* 1.3 80.7 - - - +
1433A PHE* 1.3 57.8 + - - +
1435A LYS* 2.8 52.9 + - + +
1436A SER* 3.1 9.7 + - - -
1511A MET* 4.0 24.6 - - - +
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Residues in contact with PHE1433 (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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1292A LYS 4.2 1.3 - - - -
1293A MET* 4.0 16.6 - - - -
1295A GLU* 3.1 24.5 - - - +
1337A ARG* 3.3 59.5 - - + +
1338A PRO 5.8 1.1 - - - -
1429A GLN 4.8 4.6 + - - +
1430A ILE 4.0 12.1 + - - +
1431A ILE 3.2 0.4 - - - -
1432A ASN* 1.3 77.4 - - - +
1434A TYR* 1.3 60.7 + + + +
1436A SER* 3.1 3.9 + - - -
1437A ASN* 2.8 64.5 + - + +
1438A TYR* 3.3 33.4 - + - -
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Residues in contact with TYR1434 (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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1295A GLU* 3.8 30.7 - - - +
1415A LEU* 3.1 23.9 - - + +
1416A ASP 4.8 0.2 + - - -
1418A HIS* 3.6 32.4 - + + -
1420A ARG* 5.8 2.4 + - - -
1421A PHE* 3.5 35.0 - + + -
1430A ILE* 3.7 20.9 - - + -
1431A ILE 3.0 8.1 + - - +
1433A PHE* 1.3 78.1 - - + +
1435A LYS* 1.3 66.3 + - - +
1437A ASN 3.0 18.6 - - - +
1438A TYR* 3.5 34.2 - + + +
1439A VAL* 3.7 7.6 - - - +
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Residues in contact with LYS1435 (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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1413A PRO* 3.8 24.4 - - - +
1415A LEU* 3.3 31.9 + - + +
1431A ILE* 3.1 15.6 + - + +
1432A ASN* 2.8 46.3 + - + +
1434A TYR* 1.3 78.4 - - - +
1436A SER* 1.3 60.1 + - - +
1439A VAL* 4.1 3.8 - - - +
1507A GLU* 4.3 18.4 + - - -
1511A MET* 5.2 7.0 - - - -
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Residues in contact with SER1436 (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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1339A LYS* 3.3 40.1 - - - +
1340A PRO* 4.1 4.1 - - - +
1342A TYR* 2.9 28.0 + - - -
1413A PRO* 4.1 12.6 - - - -
1432A ASN 3.1 7.9 + - - -
1433A PHE* 3.1 4.6 + - - -
1435A LYS* 1.3 80.9 - - - +
1437A ASN* 1.3 70.1 + - - +
1439A VAL* 4.4 3.6 - - - -
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Residues in contact with ASN1437 (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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1293A MET* 4.7 4.4 - - + +
1337A ARG 5.7 0.6 + - - -
1338A PRO 5.3 0.8 + - - -
1339A LYS* 5.5 1.2 - - - +
1340A PRO* 3.6 18.6 - - - +
1342A TYR* 3.9 4.7 - - - -
1364A ARG* 3.0 28.8 + - - +
1433A PHE* 2.8 74.2 + - + +
1434A TYR* 3.0 22.7 + - - +
1436A SER* 1.3 81.5 - - - +
1438A TYR* 1.3 75.3 + - + +
1439A VAL* 3.4 3.1 - - - +
1476A PRO* 4.9 0.2 - - - -
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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