Contacts of the helix formed by residues 1031 - 1039 (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 ASN1031 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1024J ALA* 5.4 2.5 - - - -
1030J GLY* 1.3 74.1 - - - +
1032J PRO* 1.4 76.3 - - + +
1033J GLN* 2.8 41.1 + - - +
1034J GLN* 2.8 53.6 + - - +
1035J ILE* 3.1 15.8 + - - +
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Residues in contact with PRO1032 (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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1004J THR* 4.6 6.3 - - + +
1008J PHE* 3.5 40.3 - - + -
1024J ALA* 5.8 3.4 - - + -
1031J ASN* 1.4 88.1 - - + +
1033J GLN* 1.3 59.7 + - + +
1035J ILE* 3.6 4.9 + - + +
1036J ARG* 2.9 28.6 + - - +
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Residues in contact with GLN1033 (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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1004J THR* 6.0 0.2 - - - -
1031J ASN* 2.8 18.8 + - - +
1032J PRO* 1.3 72.2 - - + +
1034J GLN* 1.3 60.0 + - - +
1036J ARG* 3.2 36.1 + - - +
1037J GLN* 2.9 36.7 + - - +
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Residues in contact with GLN1034 (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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877I PRO 4.1 9.4 - - - +
878I SER* 2.7 41.4 + - - +
880I MET* 3.8 21.5 - - - +
1030J GLY* 3.2 10.4 - - - -
1031J ASN* 2.8 46.8 + - - +
1033J GLN* 1.3 78.5 - - + +
1035J ILE* 1.3 60.0 + - + +
1037J GLN* 3.2 8.1 + - - +
1038J LEU* 2.9 33.8 + - - +
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Residues in contact with ILE1035 (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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877I PRO* 4.6 10.3 - - + -
1007J VAL* 4.3 8.1 - - + -
1008J PHE* 5.0 7.0 - - + -
1011J PHE* 4.1 19.7 - - + -
1020J LEU* 3.6 54.7 - - + +
1021J TYR* 5.8 1.3 - - - +
1024J ALA* 4.3 16.8 - - + -
1029J ARG 5.4 0.4 - - - +
1030J GLY* 4.8 7.0 - - - -
1031J ASN 3.1 18.4 + - - +
1032J PRO* 3.9 7.9 - - + +
1034J GLN* 1.3 77.6 - - + +
1036J ARG* 1.3 55.6 + - - +
1038J LEU* 3.0 5.4 + - + -
1039J CYS* 2.6 40.5 + - + +
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Residues in contact with ARG1036 (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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1000J THR* 3.8 25.1 - - + +
1003J VAL* 5.2 0.4 - - + -
1004J THR* 3.2 41.3 + - + +
1007J VAL* 5.0 6.9 - - - +
1008J PHE* 6.1 0.2 - - - -
1032J PRO 2.9 19.9 + - - +
1033J GLN* 3.2 41.5 + - - +
1035J ILE* 1.3 77.3 - - - +
1037J GLN* 1.3 82.7 + - - +
1039J CYS* 4.9 0.4 - - - -
1040J GLY* 2.8 39.9 + - - +
1041J MET 3.2 13.7 + - - +
1042J ARG 4.1 7.0 + - - -
1043J GLY* 5.5 0.4 - - - -
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Residues in contact with GLN1037 (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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880I MET* 3.2 35.5 - - + +
1033J GLN* 2.9 21.1 + - - +
1034J GLN* 3.2 3.4 + - - +
1036J ARG* 1.3 92.2 - - - +
1038J LEU* 1.3 53.6 + - - +
1040J GLY 4.1 0.2 - - - -
1042J ARG* 3.2 68.7 + - + +
1045J MET* 4.7 2.4 - - - +
1060J SER* 2.7 22.1 + - - -
1061J PHE* 3.2 18.1 + - - -
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Residues in contact with LEU1038 (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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876I VAL 4.8 0.2 - - - +
877I PRO* 3.3 42.2 - - + +
880I MET* 3.7 28.5 - - + -
882I LEU* 3.8 23.7 - - + +
954J ALA* 3.9 20.5 - - + +
1020J LEU* 4.7 15.5 - - + -
1034J GLN 2.9 21.0 + - - +
1035J ILE* 3.0 8.0 + - + +
1037J GLN* 1.3 75.6 - - - +
1039J CYS* 1.3 56.3 + - - +
1060J SER* 3.0 11.4 + - - -
1061J PHE* 3.7 24.0 - - + -
1062J ARG* 3.9 9.5 + - - +
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Residues in contact with CYS1039 (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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954J ALA 3.3 11.9 - - - +
955J VAL 3.1 28.3 - - - -
956J ILE* 4.1 19.6 - - - +
957J PRO* 3.6 8.7 - - - -
1007J VAL* 3.6 32.3 - - + -
1010J ASN* 6.4 0.2 - - - -
1011J PHE* 4.1 9.6 - - + -
1020J LEU* 5.2 1.6 - - + -
1035J ILE* 2.6 22.3 + - + +
1038J LEU* 1.3 76.5 - - - +
1040J GLY* 1.3 64.5 + - - +
1060J SER* 3.3 10.9 + - - -
1062J ARG* 5.2 0.4 - - - -
1063J GLU* 4.2 0.9 - - - +
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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