Contacts of the helix formed by residues 70 - 79 (chain J) in PDB entry 4XX1
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 LEU 70 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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47J ASN* 3.5 29.0 + - + +
48J TRP* 4.5 20.9 - - + +
49J MET* 4.4 13.3 - - + +
68J LEU 3.1 0.6 + - - -
69J PRO* 1.3 76.3 - - + +
71J GLY* 1.3 62.6 + - - +
72J VAL* 3.2 3.1 - - - +
73J ASP* 3.2 43.7 + - - +
74J CYS* 3.3 9.2 + - - +
92O SER* 3.2 24.2 - - - +
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Residues in contact with GLY 71 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49J MET* 4.8 8.7 - - - +
66J MET 3.1 22.9 - - - +
68J LEU* 2.6 21.4 + - - -
69J PRO 3.1 3.8 + - - -
70J LEU* 1.3 74.4 - - - +
72J VAL* 1.3 59.1 + - - +
74J CYS* 3.7 0.7 + - - +
75J TRP* 3.4 14.7 + - - +
106M PHE* 3.6 14.7 - - - -
107M TYR* 4.8 10.8 - - - -
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Residues in contact with VAL 72 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66J MET* 4.3 5.2 - - + +
67J PHE* 3.7 40.4 - - + -
68J LEU 3.8 3.1 + - - +
70J LEU* 3.2 0.6 - - - +
71J GLY* 1.3 74.5 - - - +
73J ASP* 1.3 60.4 + - - +
75J TRP* 2.9 10.6 + - + +
76J ILE* 2.7 44.3 + - + +
244J ARG* 4.0 11.4 - - + +
245J ILE* 3.7 25.4 - - + -
246J THR 6.0 0.4 - - - +
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Residues in contact with ASP 73 (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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46J VAL* 4.7 9.5 - - + +
47J ASN* 3.5 14.0 + - - +
70J LEU* 3.2 42.1 + - - +
72J VAL* 1.3 79.7 + - - +
74J CYS* 1.3 62.5 + - - +
76J ILE* 3.3 11.2 + - - +
77J ASP* 3.2 20.4 + - - +
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Residues in contact with CYS 74 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46J VAL* 5.4 0.2 - - - -
47J ASN* 3.1 22.0 - - - -
49J MET* 4.0 3.4 - - - -
50J CYS* 2.0 58.3 - - - -
70J LEU 3.3 5.5 + - - +
71J GLY 3.9 4.0 - - - +
72J VAL 3.3 0.4 - - - -
73J ASP* 1.3 78.4 - - - +
75J TRP* 1.3 58.6 + - - +
77J ASP* 3.0 6.0 + - - +
78J ASN* 2.9 34.0 + - - +
106M PHE* 3.6 22.2 - - + -
107M TYR* 4.7 5.2 - - + -
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Residues in contact with TRP 75 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60J ILE* 3.0 36.2 + - + -
61J TRP* 3.6 27.0 - + - +
66J MET* 3.4 17.9 - - + -
71J GLY 3.4 5.6 + - - +
72J VAL* 2.9 12.2 + - + +
74J CYS* 1.3 79.8 - - - +
76J ILE* 1.3 65.3 + - + +
78J ASN* 4.3 3.8 - - - +
79J THR* 2.7 69.4 + - + +
146J TRP* 4.3 22.4 - + - -
245J ILE* 3.7 33.9 - - + -
247J THR* 3.9 20.4 - - - -
106M PHE* 3.4 23.5 - + + -
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Residues in contact with ILE 76 (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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72J VAL* 2.7 24.4 + - + +
73J ASP* 3.4 13.2 - - - +
75J TRP* 1.3 96.4 - - + +
77J ASP* 1.3 60.1 + - - +
79J THR* 3.6 3.7 + - - +
80J ARG* 2.8 34.2 + - + +
246J THR* 4.0 18.8 - - - +
247J THR* 3.8 30.5 - - + +
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Residues in contact with ASP 77 (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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42J LYS* 3.2 24.3 + - - +
44J ASP* 4.1 1.4 - - - +
46J VAL* 3.2 38.3 + - + +
50J CYS* 5.4 3.2 - - - -
53J LYS* 5.1 0.2 + - - -
73J ASP 3.2 6.9 + - - +
74J CYS* 3.0 9.4 + - - +
76J ILE* 1.3 82.6 - - + +
78J ASN* 1.3 69.5 + - - +
80J ARG* 3.1 47.0 + - - +
93J ALA* 3.7 7.3 - - - +
96J VAL* 4.8 0.3 - - - +
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Residues in contact with ASN 78 (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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40J LEU* 5.0 4.5 - - + -
50J CYS* 5.3 2.8 - - - -
53J LYS* 2.4 31.1 + - - +
60J ILE* 4.8 9.1 - - + +
74J CYS* 2.9 22.4 + - - +
75J TRP* 4.0 4.4 - - - +
77J ASP* 1.3 85.7 - - - +
79J THR* 1.3 63.1 + - + +
80J ARG 3.0 10.6 + - - +
93J ALA* 4.1 1.9 + - - +
96J VAL* 3.7 36.1 - - + +
98J ILE* 5.8 1.7 - - - +
147J ARG* 5.1 1.9 + - - -
106M PHE* 3.3 39.8 - - - +
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Residues in contact with THR 79 (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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60J ILE* 4.8 16.2 - - + -
75J TRP* 2.7 66.6 + - + +
76J ILE* 3.6 5.7 + - - +
78J ASN* 1.3 76.4 - - + +
80J ARG* 1.3 64.4 + - - +
81J VAL* 3.6 5.9 - - - +
98J ILE* 6.5 0.2 - - - -
146J TRP* 6.0 1.6 - - + -
147J ARG* 3.2 35.4 + - - +
247J THR* 5.2 3.5 + - - +
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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