Contacts of the strand formed by residues 78 - 83 (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 VAL 78 (chain J).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18I LEU* 3.8 28.7 - - + -
19I TRP* 3.3 30.7 - - - +
20I GLY* 3.8 11.2 - - - +
115I LEU 4.5 0.2 - - - +
116I SER* 3.3 33.9 - - - -
117I GLY 4.7 0.7 - - - +
63J GLU* 3.1 4.1 - - - -
64J ILE* 2.7 41.6 + - + +
76J GLN 4.4 7.2 - - - +
77J PRO* 1.3 75.4 - - - +
79J THR* 1.3 62.7 + - - +
80J ILE* 3.5 6.5 + - + +
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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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48I THR* 3.8 2.4 + - - -
50I CYS* 3.8 25.7 - - + -
114I PHE* 3.6 28.5 - - + +
115I LEU 4.6 3.1 + - - -
116I SER* 3.1 22.5 + - - -
61J ARG* 2.7 55.5 + - + -
62J VAL 3.7 4.3 - - - +
63J GLU* 4.1 4.3 + - - +
77J PRO 4.1 2.1 + - - -
78J VAL* 1.3 73.0 - - - +
80J ILE* 1.3 61.5 + - - +
81J ALA 4.0 4.3 - - - +
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Residues in contact with ILE 80 (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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48I THR* 3.0 26.0 + - + +
50I CYS* 3.8 1.8 - - - -
90I MET* 3.4 8.5 - - - +
116I SER* 4.2 13.7 - - - +
46J LEU* 4.0 11.0 - - + -
49J ILE* 3.8 22.9 - - + -
62J VAL* 2.9 30.1 + - + +
63J GLU 4.7 0.2 - - - +
64J ILE* 3.6 30.5 - - + -
78J VAL* 3.5 7.2 + - + +
79J THR* 1.3 79.7 - - - +
81J ALA* 1.3 64.3 + - - +
93J MET* 3.8 8.7 - - - +
104J PHE* 3.9 27.1 - - + -
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Residues in contact with ALA 81 (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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50I CYS* 3.6 9.3 - - - -
90I MET* 3.6 14.6 - - + -
49J ILE* 3.9 24.7 - - + -
60J HIS 4.0 0.2 - - - +
61J ARG* 3.3 7.4 - - - +
62J VAL* 2.9 35.6 + - + -
79J THR* 4.4 0.4 - - - -
80J ILE* 1.3 85.0 - - + +
82J SER* 1.3 62.2 + - - +
83J LEU* 4.6 7.9 - - + -
91J VAL* 4.2 7.6 - - + -
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Residues in contact with SER 82 (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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50I CYS* 3.4 18.1 - - - +
51I LEU 2.8 27.8 + - - -
89I PRO* 3.7 19.5 - - - +
90I MET* 3.4 24.7 - - - +
59J MET* 4.0 11.4 - - - -
60J HIS 3.2 8.7 - - - -
61J ARG* 3.7 12.3 - - - -
81J ALA* 1.3 73.3 + - - +
83J LEU* 1.3 64.7 + - - +
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Residues in contact with LEU 83 (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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89I PRO* 4.6 3.6 - - - -
90I MET* 4.1 0.7 - - - -
49J ILE* 3.5 42.8 - - + +
50J CYS 4.2 0.2 - - - +
51J LEU* 3.9 29.2 - - + -
59J MET* 3.7 3.3 - - - +
60J HIS* 2.9 35.2 + - + +
62J VAL* 5.9 2.5 - - + -
81J ALA* 4.6 5.6 - - + -
82J SER* 1.3 84.6 - - - +
84J GLN* 1.3 63.7 + - - +
88J LEU* 3.5 26.0 - - + +
89J PRO 4.1 5.8 - - - +
90J MET 3.7 21.8 - - - -
91J VAL* 4.0 10.1 - - + +
113J VAL* 4.8 1.6 - - + -
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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