Contacts of the strand formed by residues 60 - 65 (chain J) in PDB entry 3T30
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 HIS 60 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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51J LEU* 3.9 20.3 - - + +
55J ALA* 4.1 12.7 - - + +
56J LYS 4.0 11.7 - - - -
58J GLU* 2.7 49.9 + - - -
59J MET* 1.3 76.3 - - - +
61J ARG* 1.3 60.2 - - - +
62J VAL* 5.3 2.4 - - + +
81J ALA 4.0 0.2 - - - +
82J SER* 3.2 4.3 - - - -
83J LEU* 2.9 42.4 + - + +
106J LEU* 4.3 3.4 - - + -
108J ALA 3.2 5.4 - - - +
109J GLY* 3.7 9.4 - - - -
111J GLY* 3.0 34.2 + - - -
113J VAL* 3.5 23.6 - - + -
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Residues in contact with ARG 61 (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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51I LEU 4.4 3.4 - - - -
53I GLU* 2.7 43.9 + - - +
114I PHE* 3.7 32.2 - - - -
59J MET* 5.5 1.1 - - + -
60J HIS* 1.3 75.4 - - - +
62J VAL* 1.3 68.3 + - - +
63J GLU* 3.1 19.4 + - + -
79J THR* 2.7 47.2 + - + -
81J ALA 3.3 11.2 - - - +
82J SER* 3.7 12.3 - - - +
106J LEU* 3.7 2.3 - - - +
107J ARG* 2.8 55.5 + - - +
108J ALA* 2.9 15.6 + - + +
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Residues in contact with VAL 62 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23J LEU* 4.5 9.0 - - + -
49J ILE* 4.4 20.9 - - + -
60J HIS* 5.3 2.5 - - + -
61J ARG* 1.3 78.8 - - - +
63J GLU* 1.3 68.1 + - - +
79J THR* 3.7 3.6 - - - +
80J ILE* 2.9 47.6 + - + -
81J ALA* 2.9 18.6 + - + +
83J LEU* 5.9 2.0 - - + -
104J PHE* 4.6 2.0 - - + -
105J GLN 3.3 12.1 - - - +
106J LEU* 4.3 14.1 - - + -
113J VAL* 4.5 8.5 - - + -
115J LEU* 4.5 15.5 - - + -
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Residues in contact with GLU 63 (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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114I PHE* 5.8 0.2 - - - -
61J ARG* 3.1 26.3 + - - +
62J VAL* 1.3 81.5 - - - +
64J ILE* 1.3 64.4 + - - +
65J LEU* 4.0 5.5 - - + +
77J PRO* 3.7 33.9 - - + +
78J VAL 3.1 9.9 - - - +
79J THR* 4.1 5.8 + - - +
80J ILE* 4.8 0.4 - - - -
104J PHE* 3.5 4.2 - - - -
105J GLN* 2.8 47.4 + - - +
107J ARG* 3.2 42.8 + - + +
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Residues in contact with ILE 64 (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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18I LEU* 3.5 26.9 - - + +
46J LEU* 5.6 0.7 - - + -
63J GLU* 1.3 75.7 - - - +
65J LEU* 1.3 70.3 + - - +
66J PRO* 3.8 0.9 - - - +
77J PRO* 3.5 3.1 - - - +
78J VAL* 2.7 39.9 + - + +
80J ILE* 3.6 37.9 - - + +
96J VAL* 6.1 0.7 - - + -
98J LEU* 4.0 37.5 - - + -
102J VAL* 4.1 14.6 - - + -
103J THR 3.5 9.2 - - - +
104J PHE* 4.0 11.4 - - + -
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Residues in contact with LEU 65 (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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18I LEU* 4.7 0.8 - - - +
29J THR* 4.6 2.7 - - + -
63J GLU* 4.0 4.0 - - + +
64J ILE* 1.3 86.9 - - - +
66J PRO* 1.3 75.1 - - + +
67J PRO 4.5 2.4 - - - +
77J PRO* 3.7 28.3 - - + -
101J PRO 5.7 0.2 - - - +
102J VAL* 5.5 0.7 - - - -
103J THR* 2.9 44.2 + - + +
105J GLN* 3.7 50.0 - - + +
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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