Contacts of the helix formed by residues 93 - 103 (chain J) in PDB entry 4DVQ
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 93 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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77J PRO* 3.5 32.3 - - + -
91J VAL 3.8 1.2 - - - -
92J MET* 1.3 84.5 - - - +
94J PRO* 1.4 68.6 - - + +
95J GLU* 4.2 15.3 - - + +
96J ASP* 3.2 25.7 + - - +
97J VAL* 3.2 16.9 - - - +
393J GLN* 3.8 24.2 - - - +
405J VAL* 5.0 0.7 - - - +
410J LEU* 4.1 3.0 - - - +
413J ASN* 3.4 29.8 - - - +
416J LEU* 3.7 14.8 - - + -
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Residues in contact with PRO 94 (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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93J LEU* 1.4 82.3 - - + +
95J GLU* 1.3 59.0 + - + +
97J VAL* 2.7 33.0 + - + +
98J GLU* 2.9 13.0 + - - +
410J LEU* 3.6 17.0 - - + -
416J LEU* 3.3 30.5 - - + -
417J PHE* 6.2 0.2 - - + -
438J PHE* 3.9 18.5 - - + +
439J HIS* 3.5 41.3 - - + +
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Residues in contact with GLU 95 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93J LEU* 4.2 16.4 - - + +
94J PRO* 1.3 78.3 - - + +
96J ASP* 1.3 75.6 + - - +
98J GLU* 3.2 11.3 + - - +
99J LYS* 3.0 42.1 + - + +
393J GLN* 3.5 26.4 + - - -
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Residues in contact with ASP 96 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77J PRO 4.0 4.3 - - - +
91J VAL* 3.4 44.3 - - + +
93J LEU* 3.3 24.7 + - - +
94J PRO 3.1 0.8 - - - -
95J GLU* 1.3 79.8 - - - +
97J VAL* 1.3 60.5 + - - +
99J LYS* 5.1 1.6 - - - +
100J LEU* 3.2 23.4 + - - +
392J LEU* 3.6 30.7 - - + +
393J GLN* 2.8 32.2 + - - +
403J VAL* 6.0 0.2 - - - +
405J VAL* 5.4 0.6 - - - +
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Residues in contact with VAL 97 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93J LEU 3.2 17.7 - - - +
94J PRO* 2.7 23.0 + - + +
96J ASP* 1.3 69.8 - - - +
98J GLU* 1.3 62.3 + - - +
100J LEU* 3.1 6.4 + - - +
101J GLN* 3.0 21.0 + - - +
382J LEU* 4.5 3.8 - - + -
405J VAL* 4.0 25.6 - - + -
410J LEU* 4.2 7.9 - - + -
438J PHE* 4.0 14.5 - - + -
441J VAL* 4.1 14.6 - - + -
445J PHE* 3.3 40.0 - - + -
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Residues in contact with GLU 98 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94J PRO 2.9 9.7 + - - +
95J GLU* 3.6 13.5 - - - +
97J VAL* 1.3 77.2 - - - +
99J LYS* 1.3 64.5 + - + +
101J GLN* 3.0 13.5 + - - +
102J GLN* 3.1 33.3 + - + +
438J PHE* 3.5 43.7 - - + +
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Residues in contact with LYS 99 (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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95J GLU* 3.0 33.0 + - + +
96J ASP* 4.9 2.0 - - - +
98J GLU* 1.3 77.0 - - + +
100J LEU* 1.3 62.1 + - - +
102J GLN* 3.5 21.3 + - - +
103J VAL 3.5 14.7 + - - -
390J LEU* 3.7 18.2 - - + +
391J VAL* 3.2 34.2 + - - +
392J LEU* 3.8 24.4 - - + +
393J GLN 4.6 4.8 - - - +
394J ASN 5.4 0.8 - - - +
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Residues in contact with LEU 100 (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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96J ASP 3.2 16.8 + - - +
97J VAL* 3.1 8.1 + - - +
99J LYS* 1.3 76.5 - - - +
101J GLN* 1.3 62.2 + - - +
103J VAL* 3.7 5.9 + - + +
104J ASP* 3.4 18.2 + - - +
383J GLU 5.6 0.4 - - - -
384J ARG* 3.7 33.4 - - + +
386J VAL* 3.3 30.3 - - + -
390J LEU* 4.5 6.9 - - + +
392J LEU* 5.2 0.7 - - + -
403J VAL* 3.5 38.8 - - + +
405J VAL* 4.7 10.8 - - + -
445J PHE* 4.1 11.9 - - + -
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Residues in contact with GLN 101 (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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97J VAL 3.0 11.7 + - - +
98J GLU 3.0 6.9 + - - +
100J LEU* 1.3 74.5 - - - +
102J GLN* 1.3 65.4 + - - +
103J VAL 3.1 2.0 - - - -
104J ASP* 2.9 36.1 + - + +
438J PHE* 3.8 22.9 - - + -
445J PHE* 4.1 10.6 - - + +
446J GLY* 3.8 29.6 + - - +
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Residues in contact with GLN 102 (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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98J GLU* 3.1 35.6 + - + +
99J LYS* 3.6 26.6 - - - +
100J LEU 3.4 0.2 - - - -
101J GLN* 1.3 76.8 - - - +
103J VAL* 1.3 57.5 + - + +
104J ASP 3.7 3.8 + - - +
390J LEU* 6.2 0.2 - - + -
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Residues in contact with VAL 103 (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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99J LYS 3.5 2.3 + - - +
100J LEU* 3.8 13.2 - - + +
101J GLN 3.1 0.4 - - - -
102J GLN* 1.3 78.2 - - - +
104J ASP* 1.3 62.7 + - - +
105J SER* 3.3 4.3 + - - -
386J VAL* 3.8 25.3 - - + +
387J SER* 4.8 8.5 + - - -
388J SER* 3.4 35.4 - - - +
389J ASP 4.7 1.8 - - - +
390J LEU* 3.1 35.9 - - + -
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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