Contacts of the helix formed by residues 1433 - 1441 (chain J) in PDB entry 4XLN
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 SER1433 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1103J HIS* 5.8 0.2 - - - -
1104J GLU* 5.7 1.6 - - - -
1431J THR* 3.2 27.0 + - - +
1432J LYS* 1.3 78.4 - - - +
1434J TRP* 1.3 61.8 + - - +
1436J SER* 3.3 20.1 + - - -
1437J ALA* 3.8 4.2 + - - +
1457J ASP* 2.4 34.7 + - - +
1460J ILE* 5.2 4.9 - - - +
1464J GLU* 3.0 34.9 + - - +
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Residues in contact with TRP1434 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1092I LEU* 4.8 10.5 - - + -
1099I VAL* 4.4 9.0 - - + -
8J VAL* 3.1 46.3 + - + -
9J ARG 4.5 0.2 - - - -
10J ILE* 3.5 43.1 - - + -
614J PHE* 5.5 3.1 - + - -
1431J THR 5.3 0.4 - - - -
1432J LYS 3.5 3.2 + - - -
1433J SER* 1.3 70.3 + - - +
1435J LEU* 1.3 92.3 + - + +
1436J SER 3.2 1.3 - - - -
1437J ALA* 3.4 2.6 + - - +
1438J ALA* 2.9 40.7 + - + +
1446J VAL* 3.9 9.8 - - + +
1447J LEU* 5.0 5.8 - - + -
1450J ALA* 4.0 12.1 - - + -
1455J LYS* 3.5 46.2 + - + +
1456J LYS 4.5 0.4 - - - -
1457J ASP* 3.3 17.9 - - + +
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Residues in contact with LEU1435 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1085I PHE* 5.1 4.7 - - + -
1088I LEU* 5.8 2.5 - - + -
8J VAL* 4.4 9.2 - - + -
614J PHE* 5.0 8.3 - - + -
1433J SER* 3.4 0.4 + - - -
1434J TRP* 1.3 117.3 - - + +
1436J SER* 1.3 56.8 + - - +
1438J ALA* 3.7 2.8 - - - +
1439J SER* 2.9 31.0 + - - -
1457J ASP* 3.3 30.9 + - + +
1459J LEU* 4.6 2.2 - - + -
1464J GLU* 3.6 16.4 - - + +
1467J ILE* 3.4 33.0 - - + +
1468J LEU* 3.9 24.0 - - + -
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Residues in contact with SER1436 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1100J ASP* 3.6 9.2 + - - -
1103J HIS* 3.3 16.4 + - - -
1428J ALA 4.6 0.3 + - - -
1431J THR* 3.7 14.6 - - - +
1433J SER* 3.3 24.1 + - - -
1434J TRP 3.2 0.4 - - - -
1435J LEU* 1.3 78.7 - - - +
1437J ALA* 1.3 57.4 + - - +
1439J SER* 2.4 18.9 + - - -
1440J PHE* 2.9 13.7 + - - +
1463J LYS* 3.1 24.3 + - - +
1464J GLU* 3.9 12.1 - - - +
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Residues in contact with ALA1437 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1428J ALA 4.3 5.8 - - - +
1429J LEU* 3.9 28.7 - - + +
1431J THR* 4.5 1.5 - - + +
1433J SER 3.8 7.9 + - - +
1434J TRP* 3.4 4.8 + - - +
1436J SER* 1.3 75.7 + - - +
1438J ALA* 1.3 64.8 + - - +
1440J PHE* 3.4 7.1 - - - +
1441J GLN 2.9 33.0 + - - +
1446J VAL* 3.7 27.1 - - + -
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Residues in contact with ALA1438 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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614J PHE* 3.4 21.2 - - + -
1434J TRP* 2.9 24.6 + - + +
1435J LEU* 3.7 9.0 - - - +
1437J ALA* 1.3 78.6 - - - +
1439J SER* 1.3 60.5 + - - +
1441J GLN 4.3 0.2 + - - -
1443J THR* 3.4 30.0 + - - +
1446J VAL* 3.9 6.0 - - + +
1447J LEU* 3.6 28.0 - - + -
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Residues in contact with SER1439 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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614J PHE* 4.1 14.0 - - - +
615J ARG* 3.7 12.3 - - - +
619J LEU* 3.6 24.1 - - - +
1096J ARG* 3.2 14.3 + - - -
1100J ASP* 4.7 0.2 - - - -
1435J LEU 2.9 14.4 + - - -
1436J SER 2.4 26.0 + - - -
1438J ALA* 1.3 77.1 - - - +
1440J PHE* 1.3 65.0 + - - +
1463J LYS* 2.5 20.3 + - - -
1467J ILE* 4.0 13.7 - - - -
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Residues in contact with PHE1440 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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615J ARG* 4.2 7.3 + - - -
1096J ARG* 3.1 34.1 + - + +
1097J LYS* 3.5 42.2 - - + -
1100J ASP* 3.2 42.4 - - + +
1425J THR* 3.9 24.5 - - + -
1428J ALA* 4.2 10.1 - - + -
1429J LEU* 3.6 24.9 - - + -
1436J SER 2.9 7.0 + - - +
1437J ALA* 3.2 9.6 + - - +
1439J SER* 1.3 81.8 + - - +
1441J GLN* 1.3 86.1 + - + +
10S A 5.5 0.7 - - - -
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Residues in contact with GLN1441 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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615J ARG* 6.0 0.2 - - - +
1097J LYS* 4.2 11.4 - - - +
1425J THR* 3.5 25.5 - - - +
1429J LEU* 3.3 11.3 - - + +
1437J ALA 2.9 15.7 + - - +
1438J ALA 4.3 0.4 + - - -
1439J SER 3.7 0.8 - - - -
1440J PHE* 1.3 111.3 - - + +
1442J ASN* 1.3 83.5 + - - +
1443J THR* 3.0 9.6 - - - +
1446J VAL* 3.9 0.3 - - - +
9S G 3.3 45.5 + - - +
10S A 4.0 3.3 + - - +
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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