Contacts of the strand formed by residues 78 - 83 (chain C) 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 C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63C GLU* 3.1 5.0 - - - -
64C ILE* 2.8 37.8 + - + +
75C MET* 4.4 10.5 - - + -
76C GLN 4.1 7.4 - - - +
77C PRO* 1.3 78.1 - - - +
79C THR* 1.3 64.0 + - - +
80C ILE* 3.6 6.3 + - + +
18D LEU* 4.2 25.4 - - + -
19D TRP 3.4 29.4 - - - +
20D GLY* 3.7 10.8 - - - +
115D LEU 4.5 0.2 - - - +
116D SER* 3.3 31.9 - - - -
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Residues in contact with THR 79 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61C ARG* 2.7 56.1 + - + -
62C VAL 3.8 3.8 - - - -
63C GLU* 3.9 6.2 + - - +
77C PRO 4.2 1.2 + - - -
78C VAL* 1.3 73.3 - - - +
80C ILE* 1.3 60.5 + - - +
81C ALA 4.1 3.6 - - - +
48D THR* 3.9 2.8 + - - +
50D CYS* 3.9 18.9 - - + -
114D PHE* 3.6 35.4 - - + +
115D LEU 4.6 3.4 + - - -
116D SER* 3.2 22.5 + - - -
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Residues in contact with ILE 80 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46C LEU* 3.9 17.3 - - + -
49C ILE* 3.9 12.6 - - + -
62C VAL* 3.0 25.8 + - + +
63C GLU 4.7 0.2 - - - +
64C ILE* 3.7 40.6 - - + -
78C VAL* 3.6 7.4 + - + +
79C THR* 1.3 77.7 - - - +
81C ALA* 1.3 64.7 + - - +
93C MET* 3.7 9.9 - - - +
104C PHE* 3.8 22.0 - - + -
18D LEU* 6.0 1.8 - - + -
47D HIS* 6.3 0.9 - - + +
48D THR* 3.0 24.6 + - + +
50D CYS* 3.7 2.0 - - - -
90D MET* 3.3 9.4 - - - +
116D SER* 4.1 15.0 - - - +
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Residues in contact with ALA 81 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49C ILE* 3.8 30.1 - - + -
60C HIS 4.5 0.2 - - - -
61C ARG* 3.3 6.8 - - - +
62C VAL* 2.9 35.7 + - + -
80C ILE* 1.3 82.5 - - - +
82C SER* 1.3 63.5 + - - +
83C LEU* 4.3 5.6 - - + -
91C VAL* 4.2 7.2 - - + -
50D CYS* 3.6 5.5 - - - -
90D MET* 3.6 17.5 - - + -
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Residues in contact with SER 82 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59C MET* 4.1 10.7 - - - -
60C HIS 3.2 8.1 - - - -
61C ARG* 3.8 12.3 - - - -
81C ALA* 1.3 74.9 + - - +
83C LEU* 1.3 64.6 + - - +
50D CYS* 3.3 19.3 - - - +
51D LEU 2.8 27.7 + - - -
89D PRO* 3.7 19.4 - - - +
90D MET* 3.4 24.0 - - - +
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Residues in contact with LEU 83 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49C ILE* 3.4 44.9 - - + +
50C CYS 4.2 1.3 - - - +
51C LEU* 4.1 24.5 - - + +
59C MET* 3.5 3.7 - - - +
60C HIS* 2.8 36.5 + - + +
62C VAL* 6.1 1.3 - - + -
81C ALA* 4.6 5.4 - - + -
82C SER* 1.3 84.2 - - - +
84C GLN* 1.3 62.9 + - - +
88C LEU* 3.5 20.9 - - + +
89C PRO 4.0 9.9 - - - +
90C MET 3.8 21.5 - - - +
91C VAL* 4.1 12.6 - - + +
113C VAL* 5.9 0.4 - - + -
89D PRO* 4.6 3.4 - - - -
90D MET* 4.1 2.9 - - - -
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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