Contacts of the helix formed by residues 1442 - 1454 (chain J) in PDB entry 4XLQ
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 ASN1442 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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108J VAL* 5.1 7.7 - - - +
608J SER* 5.6 1.4 + - - -
1429J LEU* 5.2 10.2 - - + +
1441J GLN* 1.3 83.8 - - + +
1443J THR* 1.3 65.3 + - - +
1444J THR* 3.0 15.7 + - - -
1445J HIS* 3.2 33.2 + - - +
1446J VAL* 3.4 9.0 + - - +
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Residues in contact with THR1443 (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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607J LEU* 5.4 3.8 + - + +
608J SER* 4.7 20.1 + - - -
609J GLY 5.7 0.2 + - - -
614J PHE* 5.1 12.5 - - + +
1438J ALA* 2.9 42.9 + - + +
1439J SER 5.2 0.3 - - - -
1440J PHE 5.2 0.3 - - - -
1441J GLN* 3.0 9.7 - - - -
1442J ASN* 1.3 73.9 + - - +
1444J THR* 1.3 64.6 + - - +
1446J VAL* 3.0 6.9 + - - +
1447J LEU* 2.8 46.9 + - + +
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Residues in contact with THR1444 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103J TRP* 3.0 49.9 - - + +
107J ASP* 4.8 1.1 - - - -
583J ASP* 4.2 2.2 - - - +
586J ARG* 3.9 25.5 + - - +
604J THR* 3.7 16.5 - - + +
608J SER* 4.3 12.6 + - - -
1442J ASN* 3.0 14.4 + - - -
1443J THR* 1.3 75.7 + - - +
1445J HIS* 1.3 52.6 + - - -
1447J LEU* 4.4 0.4 - - - +
1448J THR* 2.3 28.8 + - - -
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Residues in contact with HIS1445 (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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107J ASP* 3.6 15.0 + - - +
108J VAL* 4.3 19.1 - - + +
109J PRO* 3.3 29.9 - - + +
1429J LEU* 6.3 0.8 - - - +
1442J ASN* 3.2 28.8 + - - +
1444J THR* 1.3 75.8 - - - +
1446J VAL* 1.3 68.8 + - + +
1448J THR* 3.1 3.1 + - - -
1449J GLU* 3.0 54.1 + - + +
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Residues in contact with VAL1446 (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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1429J LEU* 3.5 32.1 - - + +
1434J TRP* 4.2 10.3 - - + +
1437J ALA* 4.1 14.6 - - + +
1438J ALA* 3.8 25.1 - - + +
1441J GLN 4.1 0.4 - - - +
1442J ASN* 3.4 17.7 - - - +
1443J THR* 3.0 12.8 + - - +
1445J HIS* 1.3 78.5 - - + +
1447J LEU* 1.3 67.7 + - - +
1449J GLU* 3.2 5.0 + - - +
1450J ALA* 2.9 29.3 + - + +
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Residues in contact with LEU1447 (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* 4.6 9.0 - - + -
1097I LEU* 4.4 13.9 - - + -
10J ILE* 4.2 25.5 - - + +
103J TRP* 3.3 33.7 - - + -
607J LEU* 5.0 15.9 - - + -
614J PHE* 5.0 6.3 - - + -
1434J TRP* 4.6 13.9 - - + -
1438J ALA* 4.8 4.3 - - + -
1443J THR* 2.8 42.9 + - + +
1446J VAL* 1.3 73.3 - - - +
1448J THR* 1.3 64.3 + - - +
1450J ALA* 4.5 4.5 - - - -
1451J ALA* 2.8 31.0 + - + +
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Residues in contact with THR1448 (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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103J TRP* 3.3 21.2 - - + -
104J PHE* 3.6 37.7 - - + +
107J ASP* 3.6 24.3 + - - +
111J LYS* 3.9 7.9 - - + -
1444J THR 2.3 32.1 + - - -
1445J HIS* 3.1 7.9 + - - -
1447J LEU* 1.3 78.4 - - - +
1449J GLU* 1.3 65.0 + - - +
1451J ALA* 3.8 3.3 - - - +
1452J ILE* 3.0 26.0 + - + +
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Residues in contact with GLU1449 (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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107J ASP* 4.8 0.4 - - - +
109J PRO* 3.5 18.6 - - + +
111J LYS* 3.5 21.9 + - - +
497J GLU* 5.2 3.4 - - - +
1445J HIS* 3.0 48.4 + - + +
1446J VAL* 3.8 4.6 - - - +
1448J THR* 1.3 79.4 - - - +
1450J ALA* 1.3 62.6 + - - +
1452J ILE* 3.7 8.4 - - - +
1453J ALA* 3.6 17.2 + - - +
1455J LYS* 5.3 3.7 - - - +
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Residues in contact with ALA1450 (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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10J ILE* 4.5 4.9 - - + -
1434J TRP* 3.7 34.5 - - + -
1446J VAL* 2.9 23.5 + - + +
1447J LEU* 3.8 5.2 - - - +
1449J GLU* 1.3 70.7 - - - +
1451J ALA* 1.3 55.9 + - - +
1453J ALA* 3.0 4.9 + - - +
1454J GLY 2.6 31.5 + - - -
1455J LYS* 3.4 25.4 + - + +
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Residues in contact with ALA1451 (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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1097I LEU* 4.3 16.4 - - + -
10J ILE* 3.7 20.3 - - + +
11J ALA* 3.2 28.3 - - - +
12J LEU* 3.4 22.2 + - + +
1447J LEU* 2.8 22.1 + - + +
1448J THR* 3.8 2.9 - - - +
1450J ALA* 1.3 72.6 - - - +
1452J ILE* 1.3 66.2 + - - +
1454J GLY 3.1 7.3 + - - -
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Residues in contact with ILE1452 (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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12J LEU* 3.6 22.1 - - + +
104J PHE* 4.2 6.5 - - + -
111J LYS* 3.7 24.7 - - + +
498J VAL* 4.9 1.3 - - + +
501J ALA* 4.1 14.8 - - + -
502J PHE* 3.5 34.5 - - + -
505J SER* 2.9 19.4 + - - -
507J ASN* 3.1 9.7 + - - +
512J MET* 3.6 30.7 - - + -
1448J THR* 3.0 23.0 + - - +
1449J GLU* 3.7 7.6 - - - +
1451J ALA* 1.3 80.4 - - - +
1453J ALA* 1.3 59.5 + - - +
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Residues in contact with ALA1453 (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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9J ARG* 5.7 0.2 + - - -
501J ALA* 4.0 22.4 - - + +
505J SER* 3.3 22.0 + - - -
1449J GLU 3.6 8.0 + - - +
1450J ALA 3.0 6.8 + - - +
1452J ILE* 1.3 77.8 - - - +
1454J GLY* 1.3 65.4 + - - +
1455J LYS* 3.6 12.1 + - + -
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Residues in contact with GLY1454 (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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9J ARG* 3.2 24.8 + - - -
10J ILE 3.2 20.9 - - - -
11J ALA* 3.9 9.9 - - - -
505J SER* 4.7 1.8 - - - -
1450J ALA 2.6 11.3 + - - -
1451J ALA 3.1 9.0 + - - -
1452J ILE 3.2 0.4 + - - -
1453J ALA* 1.3 76.4 - - - +
1455J LYS* 1.3 64.1 + - - -
1456J LYS* 3.3 6.1 + - - +
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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