Contacts of the strand formed by residues 78 - 83 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63B GLU* 3.1 3.6 - - - -
64B ILE* 2.7 39.1 + - + +
76B GLN 4.3 7.2 - - - +
77B PRO* 1.3 76.7 - - - +
79B THR* 1.3 61.4 + - - +
80B ILE* 3.5 7.4 + - + +
18C LEU* 4.1 29.8 - - + +
19C TRP* 3.6 12.1 - - - +
20C GLY* 3.7 28.9 - - - +
116C SER* 3.3 34.1 - - - -
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Residues in contact with THR 79 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61B ARG* 2.8 56.1 + - + +
62B VAL 3.6 5.4 - - - +
63B GLU* 4.1 5.1 + - - +
77B PRO 4.1 1.7 + - - -
78B VAL* 1.3 71.8 - - - +
80B ILE* 1.3 61.9 + - - +
81B ALA 4.0 3.4 - - - +
20C GLY* 5.8 0.2 - - - -
48C THR* 3.9 1.7 + - - -
50C CYS* 3.9 27.0 - - + -
114C PHE* 3.7 27.3 - - + +
115C LEU 4.7 3.3 + - - -
116C SER* 3.2 22.2 + - - -
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Residues in contact with ILE 80 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46B LEU* 3.9 20.0 - - + -
49B ILE* 3.9 15.0 - - + -
62B VAL* 2.9 24.0 + - + +
64B ILE* 3.7 28.7 - - + -
78B VAL* 3.5 10.5 + - + +
79B THR* 1.3 77.8 - - - +
81B ALA* 1.3 64.8 + - - +
93B MET* 3.6 9.4 - - - +
104B PHE* 3.8 31.4 - - + -
18C LEU* 5.9 1.6 - - + -
48C THR* 3.0 31.5 + - + +
50C CYS* 3.7 2.2 - - - -
90C MET* 3.6 1.7 - - - +
116C SER* 4.2 9.4 - - - +
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Residues in contact with ALA 81 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49B ILE* 3.7 32.5 - - + -
60B HIS 5.3 0.2 - - - -
61B ARG* 3.3 6.9 - - - +
62B VAL* 3.0 34.8 + - + +
79B THR* 3.7 0.4 - - - -
80B ILE* 1.3 82.5 - - + +
82B SER* 1.3 63.7 + - - +
83B LEU* 4.7 4.9 - - + -
91B VAL* 4.3 4.7 - - + -
93B MET* 4.3 1.6 - - + -
50C CYS* 3.6 8.6 - - - -
90C MET* 3.6 14.4 - - + -
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Residues in contact with SER 82 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59B MET* 3.5 19.7 - - - +
60B HIS 3.2 5.6 - - - -
61B ARG* 3.8 7.4 - - - -
81B ALA* 1.3 75.8 + - - +
83B LEU* 1.3 62.3 + - - +
50C CYS* 3.2 18.3 - - - +
51C LEU 2.8 27.5 + - - -
89C PRO* 3.6 19.1 - - - +
90C MET* 3.3 27.2 - - - +
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Residues in contact with LEU 83 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49B ILE* 3.5 43.7 - - + +
50B CYS 4.2 1.8 - - - +
51B LEU* 4.0 26.0 - - + +
59B MET* 3.5 4.1 - - - +
60B HIS* 2.7 36.5 + - + +
62B VAL* 6.0 1.1 - - + -
81B ALA* 4.7 3.1 - - + -
82B SER* 1.3 85.1 - - - +
84B GLN* 1.3 62.7 + - - +
88B LEU* 3.8 19.1 - - + +
89B PRO 4.1 7.6 - - - +
90B MET* 3.6 28.7 - - - -
91B VAL* 3.9 10.1 - - + +
113B VAL* 4.8 1.3 - - + -
89C PRO* 4.6 3.6 - - - -
90C MET* 4.2 0.9 - - - -
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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