Contacts of the strand formed by residues 60 - 65 (chain F) 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 F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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51F LEU* 3.8 28.3 - - + +
55F ALA* 4.0 11.4 - - + +
56F LYS 3.7 18.1 + - - -
58F GLU* 2.8 39.6 + - - -
59F MET* 1.3 76.2 - - - +
61F ARG* 1.3 60.9 + - - +
62F VAL* 5.5 2.7 - - + -
81F ALA 3.9 0.4 - - - +
82F SER* 3.2 5.2 - - - -
83F LEU* 2.9 38.5 + - + +
85F ALA 5.9 0.2 - - - -
106F LEU* 4.2 12.1 - - + -
108F ALA 3.1 6.5 - - - +
109F GLY* 3.8 9.0 - - - -
110F SER 3.5 2.8 + - - -
111F GLY* 2.9 39.7 + - - -
113F VAL* 4.9 2.9 - - + -
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Residues in contact with ARG 61 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59F MET* 4.1 2.9 - - + -
60F HIS* 1.3 76.0 - - - +
62F VAL* 1.3 66.2 + - - +
63F GLU* 4.0 7.7 + - - -
79F THR* 2.8 38.8 + - + -
81F ALA 3.2 9.9 - - - +
82F SER* 3.9 9.6 - - - +
106F LEU* 3.7 3.5 - - - +
107F ARG* 2.9 71.4 + - + +
108F ALA* 3.0 15.7 + - + +
52J GLY* 4.3 3.7 - - - -
53J GLU* 2.7 44.3 + - - +
114J PHE* 3.7 31.0 - - - -
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Residues in contact with VAL 62 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23F LEU* 4.2 16.8 - - + -
49F ILE* 4.5 8.5 - - + -
60F HIS* 5.5 2.0 - - + -
61F ARG* 1.3 80.5 - - - +
63F GLU* 1.3 68.0 + - - +
79F THR* 3.6 4.0 - - - +
80F ILE* 2.8 47.8 + - + -
81F ALA* 2.8 19.4 + - + +
83F LEU* 6.0 1.1 - - + -
104F PHE* 4.5 3.6 - - + -
105F GLN 3.5 8.1 - - - +
106F LEU* 4.1 12.1 - - + -
113F VAL* 4.1 27.1 - - + -
115F LEU* 4.4 11.9 - - + -
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Residues in contact with GLU 63 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61F ARG* 4.0 5.0 + - - +
62F VAL* 1.3 78.6 - - - +
64F ILE* 1.3 64.5 + - - +
65F LEU* 3.5 13.3 - - + +
77F PRO* 3.3 20.6 - - + +
78F VAL 3.1 17.5 - - - +
79F THR* 4.2 5.9 + - - +
80F ILE 4.3 0.2 - - - +
104F PHE* 3.4 4.5 - - - -
105F GLN* 2.9 58.9 + - + +
107F ARG* 2.9 54.6 + - + +
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Residues in contact with ILE 64 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46F LEU* 5.6 0.2 - - + -
63F GLU* 1.3 76.6 - - - +
65F LEU* 1.3 71.7 + - - +
66F PRO* 4.0 0.5 - - - +
77F PRO* 3.2 4.3 - - - +
78F VAL* 2.7 35.3 + - - +
80F ILE* 3.7 36.1 - - + -
96F VAL* 6.3 0.4 - - + -
98F LEU* 3.7 33.7 - - + -
102F VAL* 3.8 14.6 - - + -
103F THR 3.3 9.2 - - - +
104F PHE* 3.9 11.2 - - + -
18J LEU* 3.5 33.2 - - + +
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Residues in contact with LEU 65 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29F THR* 4.9 3.6 - - + -
63F GLU* 3.5 27.6 - - + +
64F ILE* 1.3 80.3 - - - +
66F PRO* 1.3 76.2 - - + +
67F PRO* 3.7 3.1 - - - +
77F PRO* 3.6 21.8 - - + -
103F THR* 2.9 43.9 + - + +
105F GLN* 3.2 37.9 - - + +
18J LEU* 6.2 0.7 - - - -
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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