Contacts of the helix formed by residues 1083 - 1095 (chain I) 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 GLU1083 (chain I).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1017I THR* 5.1 0.2 - - - +
1018I GLN* 3.6 27.6 - - + +
1058I ASP* 3.1 19.1 - - + +
1060I ILE* 3.2 12.5 - - + +
1081I VAL* 3.0 8.3 + - - +
1082I PRO* 1.3 73.4 - - - +
1084I SER* 1.3 55.1 + - - +
1085I PHE 2.6 3.7 + - - -
1086I ARG* 2.3 64.1 + - - +
1087I VAL* 3.2 17.4 + - + +
84J ILE* 5.5 0.3 - - - +
87J ARG* 3.2 28.2 - - - +
88J TYR* 2.5 31.6 + - - -
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Residues in contact with SER1084 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1017I THR* 3.1 29.6 - - - -
1058I ASP* 2.6 23.3 + - - -
1082I PRO 3.0 2.1 + - - -
1083I GLU* 1.3 76.3 - - - +
1085I PHE* 1.3 57.6 + - - +
1087I VAL* 3.5 17.0 - - - +
1088I LEU* 2.9 27.2 + - - +
613J ARG* 4.6 5.0 - - - +
617J ASN* 3.2 21.5 + - - -
618J LEU* 3.9 7.4 - - - +
621J LYS* 4.0 3.6 + - - -
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Residues in contact with PHE1085 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1081I VAL* 6.5 0.2 - - + -
1082I PRO* 3.6 31.7 - - + +
1083I GLU 2.6 5.1 + - - -
1084I SER* 1.3 76.3 + - - +
1086I ARG* 1.3 64.3 - - + +
1088I LEU* 3.1 17.0 + - + +
1089I VAL* 2.9 48.0 + - + +
1101I THR* 4.7 10.1 - - + -
1111I ILE* 4.1 16.6 - - + -
8J VAL* 4.9 8.1 - - + -
618J LEU* 4.3 6.3 - - + +
1435J LEU* 5.1 5.4 - - + -
1467J ILE* 3.4 36.3 - - + +
1468J LEU* 3.5 43.5 - - + -
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Residues in contact with ARG1086 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1060I ILE* 3.3 28.1 - - - +
1081I VAL* 3.4 31.1 - - + +
1082I PRO* 5.5 0.4 - - + -
1083I GLU* 2.3 53.1 + - - +
1085I PHE* 1.3 69.8 - - + +
1087I VAL* 1.3 59.4 + - - +
1089I VAL* 3.0 11.8 + - - +
1090I LYS* 2.9 29.9 + - - +
1111I ILE* 3.2 47.0 + - + +
1112I PHE* 4.2 10.1 + - + +
1113I GLU* 3.5 20.6 + - - +
1115I LEU* 5.3 0.8 - - - +
88J TYR* 2.7 38.6 + - + -
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Residues in contact with VAL1087 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1016I ILE* 4.4 9.9 - - + +
1017I THR* 5.3 2.2 - - - -
1083I GLU* 3.2 25.3 + - + +
1084I SER* 3.5 21.5 - - - +
1086I ARG* 1.3 75.5 - - - +
1088I LEU* 1.3 58.3 + - - +
1090I LYS* 4.0 1.8 - - - +
1091I GLU* 2.9 53.3 + - + +
87J ARG* 3.7 17.7 - - + +
88J TYR* 5.3 1.1 - - + -
524J LEU* 3.7 30.7 - - + +
613J ARG* 5.2 6.1 - - - +
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Residues in contact with LEU1088 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1084I SER 2.9 15.2 + - - +
1085I PHE* 3.1 26.7 - - + +
1087I VAL* 1.3 77.7 - - - +
1089I VAL* 1.3 55.6 + - + +
1091I GLU* 3.2 8.3 + - - +
1092I LEU* 2.9 54.6 + - + +
607J LEU* 3.6 26.2 - - + -
613J ARG* 3.8 23.6 - - + -
614J PHE* 3.7 36.6 - - + -
618J LEU* 4.4 6.1 - - + -
1434J TRP* 6.3 0.2 - - + -
1435J LEU* 5.8 3.4 - - + -
1467J ILE* 5.5 0.2 - - + -
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Residues in contact with VAL1089 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1085I PHE* 2.9 47.2 + - + +
1086I ARG* 3.0 8.5 + - - +
1088I LEU* 1.3 78.3 - - + +
1090I LYS* 1.3 57.4 + - - +
1092I LEU* 3.0 10.7 + - + +
1093I GLN* 2.9 34.6 + - + +
1099I VAL* 3.6 33.7 - - + +
1101I THR* 6.0 1.6 - - + -
1111I ILE* 3.8 11.9 - - + -
1112I PHE* 3.6 23.6 - - + -
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Residues in contact with LYS1090 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1086I ARG 2.9 12.9 + - - +
1087I VAL* 4.0 0.4 - - - +
1089I VAL* 1.3 76.6 - - - +
1091I GLU* 1.3 58.0 + - - +
1093I GLN* 3.0 24.2 + - + +
1094I ALA 2.9 23.7 + - - -
1112I PHE* 3.3 45.9 - - + -
1116I ALA* 4.8 7.4 - - - +
21J TRP* 5.9 1.2 - - - -
87J ARG 5.0 0.2 - - - +
88J TYR* 3.3 33.7 - - + +
90J MET* 3.6 37.4 - - + +
520J LEU* 3.4 9.3 - - + +
524J LEU* 3.8 20.9 - - + -
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Residues in contact with GLU1091 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1087I VAL* 2.9 40.0 + - + +
1088I LEU* 3.2 19.3 + - - +
1090I LYS* 1.3 76.9 - - - +
1092I LEU* 1.3 61.0 + - - +
1094I ALA* 3.1 12.9 + - - +
1095I LEU* 3.1 20.4 - - + +
520J LEU* 3.7 28.0 - - + +
524J LEU* 4.9 0.9 - - + -
603J LEU* 4.4 4.4 - - + +
606J ILE* 3.3 34.1 - - + +
607J LEU* 4.3 9.6 - - + -
613J ARG* 3.3 24.1 + - - +
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Residues in contact with LEU1092 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1088I LEU* 2.9 37.8 + - + +
1089I VAL* 3.0 8.9 + - + +
1091I GLU* 1.3 75.6 - - - +
1093I GLN* 1.3 57.3 + - - +
1095I LEU* 2.9 22.4 + - - +
1097I LEU* 3.2 29.8 + - + +
1099I VAL* 3.7 32.8 - - + -
10J ILE* 5.0 0.4 - - + -
607J LEU* 3.6 26.7 - - + -
614J PHE* 5.4 2.5 - - + -
1434J TRP* 4.8 13.2 - - + -
1447J LEU* 3.6 29.8 - - + -
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Residues in contact with GLN1093 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1089I VAL* 2.9 23.7 + - + +
1090I LYS* 3.0 27.4 + - + +
1092I LEU* 1.3 76.5 - - - +
1094I ALA* 1.3 55.7 + - - +
1096I ALA 3.0 14.4 + - - -
1097I LEU 2.9 26.1 + - - -
1098I ASP* 3.5 10.5 + - - +
1099I VAL* 3.1 28.2 + - + +
21J TRP* 3.1 45.9 + - + -
90J MET* 3.5 22.8 - - + +
518J PRO* 3.3 6.7 - - - +
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Residues in contact with ALA1094 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1090I LYS 2.9 4.9 + - - -
1091I GLU 3.1 12.7 + - - +
1093I GLN* 1.3 76.2 - - - +
1095I LEU* 1.3 57.2 + - - +
1096I ALA 3.2 1.6 + - - -
90J MET* 4.5 2.2 - - - -
517J VAL* 5.3 1.0 - - - +
518J PRO* 3.6 27.3 - - - +
519J VAL 5.1 0.2 - - - -
520J LEU* 3.6 28.3 - - + +
544J TYR* 4.0 9.6 + - - +
582J ILE* 4.5 4.7 - - - +
603J LEU* 3.4 29.2 - - + +
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Residues in contact with LEU1095 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1091I GLU 3.1 26.7 - - - +
1092I LEU* 2.9 12.5 + - - +
1094I ALA* 1.3 76.4 - - - +
1096I ALA* 1.3 67.3 + - - +
1097I LEU* 3.5 11.7 + - + +
101J HIS* 3.0 34.9 + - + +
103J TRP* 3.5 42.0 - - + -
582J ILE* 4.5 4.0 - - + -
603J LEU* 3.5 30.1 - - + -
604J THR* 3.5 13.9 - - - +
607J LEU* 3.6 21.5 - - + -
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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