Contacts of the helix formed by residues 84 - 89 (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 ILE 84 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1060I ILE* 5.6 7.0 - - + -
1083I GLU* 5.5 0.9 - - - +
1115I LEU* 3.7 22.2 - - + -
55J ASP* 5.0 0.4 + - - -
82J ARG* 3.4 45.7 - - + +
83J SER* 1.3 79.2 + - - +
85J VAL* 1.3 60.1 + - - +
87J ARG* 2.9 43.7 + - + +
88J TYR* 3.5 29.8 - - + +
523J ASP* 6.1 0.2 - - - +
353L LEU* 4.8 17.7 - - + -
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Residues in contact with VAL 85 (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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1115I LEU* 3.7 28.0 - - + +
50J PHE 3.6 12.8 - - - +
51J GLY* 3.8 13.2 - - - -
52J PRO* 4.0 2.9 - - + -
81J THR* 3.7 28.9 - - + +
82J ARG 3.6 13.7 - - - +
83J SER 4.3 1.8 - - - -
84J ILE* 1.3 77.7 - - - +
86J ARG* 1.3 58.6 + - - +
87J ARG 2.9 0.4 - - - -
88J TYR* 2.9 9.4 + - - +
89J ARG* 2.9 61.7 + - - +
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Residues in contact with ARG 86 (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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39J PRO* 4.6 0.2 - - - +
45J PHE* 3.3 35.0 + - - +
47J GLU* 4.7 0.4 - - - +
50J PHE* 3.3 16.3 - - + +
51J GLY 3.2 31.5 + - - +
52J PRO 3.2 21.3 - - - +
53J ILE* 3.7 33.2 - - - +
83J SER 3.5 7.2 + - - +
84J ILE 3.1 1.2 + - - -
85J VAL* 1.3 74.8 - - + +
87J ARG* 1.3 56.9 + - - +
89J ARG 4.9 0.2 - - - +
521J PRO* 3.1 20.2 - - - +
522J PRO* 3.2 33.7 - - + +
523J ASP* 2.9 44.4 + - - +
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Residues in contact with ARG 87 (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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1015I LEU* 2.8 26.1 + - - +
1016I ILE 2.7 22.6 + - - -
1018I GLN* 3.0 22.7 - - - +
1083I GLU* 3.2 33.1 + - - +
1087I VAL* 3.7 8.6 - - + +
1090I LYS* 4.8 0.3 - - - +
83J SER 4.8 0.2 + - - -
84J ILE* 2.9 25.5 + - + +
86J ARG* 1.3 80.7 - - - +
88J TYR* 1.3 79.4 + - + +
521J PRO* 3.1 19.5 - - - +
523J ASP* 3.8 33.3 + - + +
524J LEU* 3.3 25.7 - - + +
350L ASP* 3.9 7.1 + - - -
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Residues in contact with TYR 88 (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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1060I ILE* 4.7 0.2 - - - +
1083I GLU* 2.5 36.7 + - - -
1086I ARG* 2.7 49.2 + - + -
1087I VAL* 5.3 1.1 - - - -
1090I LYS* 3.3 29.7 - - + -
1112I PHE* 3.5 27.4 - + + -
1115I LEU* 3.5 26.5 - - + -
1116I ALA* 3.4 18.2 - - + +
84J ILE* 3.5 40.3 - - + +
85J VAL* 2.9 5.0 + - - +
87J ARG* 1.3 88.5 - - + +
89J ARG* 1.3 60.5 + - + +
90J MET 3.8 0.5 + - - -
521J PRO* 3.8 3.8 - - - -
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Residues in contact with ARG 89 (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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1115I LEU 3.3 19.6 + - - -
1116I ALA* 4.1 9.0 - - + -
23J TYR* 3.3 53.6 + - + -
49J ILE 4.0 9.6 + - - -
50J PHE* 3.2 38.2 - - + +
51J GLY* 4.9 3.8 - - - -
79J GLU* 2.9 43.8 + - - +
81J THR* 4.6 0.6 + - - +
85J VAL* 2.9 48.6 + - + +
87J ARG 3.6 0.2 - - - -
88J TYR* 1.3 77.9 - - + +
90J MET* 1.3 59.8 + - - +
521J PRO* 3.1 15.6 - - - +
522J PRO* 4.3 0.3 - - - +
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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