Contacts of the strand formed by residues 78 - 83 (chain I) 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 I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18H LEU* 4.6 18.4 - - + +
19H TRP* 3.4 35.9 - - - +
20H GLY* 3.7 9.6 - - - +
115H LEU 4.7 0.2 - - - +
116H SER* 3.3 33.2 - - - -
117H GLY 4.7 0.4 - - - +
63I GLU* 3.0 4.3 - - - -
64I ILE* 2.7 45.8 + - + +
66I PRO* 6.1 3.1 - - + -
77I PRO* 1.3 76.6 - - + +
79I THR* 1.3 60.1 + - - +
80I ILE* 3.6 7.0 + - + +
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Residues in contact with THR 79 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48H THR* 3.9 2.8 + - - +
50H CYS* 4.0 17.9 - - + -
114H PHE* 3.6 34.2 - - + +
115H LEU 4.6 4.0 + - - -
116H SER* 3.2 21.8 + - - -
61I ARG* 2.8 55.9 + - + -
62I VAL 3.5 5.2 - - - +
63I GLU* 3.7 7.2 + - - +
77I PRO 4.2 1.2 + - - -
78I VAL* 1.3 72.2 - - - +
80I ILE* 1.3 60.4 + - - +
81I ALA 4.0 3.4 - - - +
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Residues in contact with ILE 80 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18H LEU* 5.9 0.9 - - + -
48H THR* 3.0 25.9 + - + +
50H CYS* 3.7 1.6 - - - -
90H MET* 3.4 9.0 - - - +
116H SER* 4.2 10.1 - - - +
46I LEU* 4.0 11.0 - - + -
49I ILE* 3.7 22.4 - - + -
62I VAL* 2.7 31.6 + - + +
63I GLU 4.6 0.9 - - - +
64I ILE* 3.8 26.9 - - + -
78I VAL* 4.1 10.1 - - + +
79I THR* 1.3 75.7 - - - +
81I ALA* 1.3 59.0 + - - +
93I MET* 3.7 9.6 - - - +
104I PHE* 3.8 35.0 - - + -
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Residues in contact with ALA 81 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50H CYS* 3.6 8.8 - - - -
90H MET* 3.6 14.1 - - + -
49I ILE* 3.8 30.3 - - + -
60I HIS 4.5 0.2 - - - -
61I ARG* 3.4 6.4 - - - +
62I VAL* 2.9 36.8 + - + -
79I THR* 3.8 0.4 - - - -
80I ILE* 1.3 80.5 - - - +
82I SER* 1.3 63.0 + - - +
83I LEU* 4.3 5.2 - - + -
91I VAL* 4.2 7.4 - - + -
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Residues in contact with SER 82 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50H CYS* 3.3 17.6 - - - +
51H LEU 2.8 28.0 + - - -
89H PRO* 3.6 20.0 - - - +
90H MET* 3.2 26.2 - - - +
59I MET* 4.0 11.0 - - - -
60I HIS 3.2 8.1 - - - -
61I ARG* 3.8 13.2 - - - +
81I ALA* 1.3 74.3 + - - +
83I LEU* 1.3 63.6 + - - +
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Residues in contact with LEU 83 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89H PRO* 4.7 2.9 - - - -
90H MET* 4.2 0.7 - - - -
49I ILE* 3.5 41.7 - - + +
50I CYS 4.2 2.0 - - - +
51I LEU* 3.9 23.3 - - + +
59I MET* 3.6 3.8 - - - +
60I HIS* 2.8 36.0 + - + +
62I VAL* 5.9 1.3 - - + -
81I ALA* 4.6 6.1 - - + -
82I SER* 1.3 83.5 - - - +
84I GLN* 1.3 63.4 + - - +
88I LEU* 3.4 24.5 - - + +
89I PRO 4.0 9.9 - - - +
90I MET 3.7 23.1 - - - +
91I VAL* 4.0 10.3 - - + +
113I VAL* 4.5 3.1 - - + -
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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
------------------------------------------------------------
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