Contacts of the strand formed by residues 60 - 65 (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 HIS 60 (chain I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51I LEU* 3.7 21.3 - - + +
55I ALA* 3.9 11.3 - - + +
56I LYS 3.9 12.6 - - - -
58I GLU* 2.9 47.4 + - - -
59I MET* 1.3 76.8 - - - +
61I ARG* 1.3 60.4 + - - +
62I VAL* 5.4 2.2 - - + -
81I ALA 4.0 0.3 - - - +
82I SER* 3.2 5.2 - - - -
83I LEU* 2.8 39.2 + - + +
106I LEU* 4.1 7.0 - - + -
108I ALA 3.2 4.5 - - - +
109I GLY* 3.8 8.5 - - - -
110I SER 3.5 1.2 + - - -
111I GLY* 2.8 35.9 + - - -
113I VAL* 3.4 23.3 - - + -
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Residues in contact with ARG 61 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52H GLY* 4.5 2.2 - - - -
53H GLU* 2.8 47.8 + - - +
114H PHE* 3.4 35.5 - - - -
59I MET* 5.7 0.9 - - + -
60I HIS* 1.3 75.5 - - - +
62I VAL* 1.3 61.4 + - - +
63I GLU* 3.4 17.6 + - - -
79I THR* 2.8 53.1 + - + +
81I ALA 3.4 5.4 - - - +
82I SER* 3.8 11.4 - - - +
106I LEU* 3.6 3.9 - - - +
107I ARG* 2.8 62.7 + - + +
108I ALA* 2.9 14.5 + - + +
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Residues in contact with VAL 62 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23I LEU* 4.2 17.0 - - + -
49I ILE* 4.3 9.9 - - + -
60I HIS* 5.4 1.8 - - + -
61I ARG* 1.3 79.0 - - - +
63I GLU* 1.3 64.7 + - - +
79I THR* 3.5 4.2 - - - +
80I ILE* 2.7 51.9 + - + +
81I ALA* 2.9 21.9 + - + +
83I LEU* 5.9 1.6 - - + -
104I PHE* 4.7 1.3 - - + -
105I GLN 3.4 9.6 - - - +
106I LEU* 4.2 15.3 - - + -
113I VAL* 4.2 21.5 - - + -
115I LEU* 4.6 11.0 - - + -
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Residues in contact with GLU 63 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114H PHE* 5.7 0.2 - - - -
61I ARG* 3.4 15.0 + - - +
62I VAL* 1.3 79.1 - - - +
64I ILE* 1.3 63.9 + - - +
65I LEU* 4.3 4.3 - - + -
77I PRO* 3.4 31.7 - - + +
78I VAL 3.0 9.6 - - - +
79I THR* 3.7 18.8 + - - +
80I ILE* 4.6 1.1 - - - -
104I PHE* 3.3 5.7 - - - +
105I GLN* 2.8 61.1 + - + +
107I ARG* 3.4 29.1 + - + +
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Residues in contact with ILE 64 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18H LEU* 3.6 30.7 - - + -
46I LEU* 5.6 0.9 - - + -
63I GLU* 1.3 73.2 - - - +
65I LEU* 1.3 76.1 + - - +
66I PRO* 4.0 0.7 - - - +
77I PRO* 3.3 3.3 - - - +
78I VAL* 2.7 41.5 + - + +
80I ILE* 3.8 24.7 - - + -
96I VAL* 6.1 0.4 - - + -
98I LEU* 4.0 36.6 - - + -
102I VAL* 4.1 11.7 - - + -
103I THR 3.3 10.3 - - - +
104I PHE* 3.8 24.7 - - + -
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Residues in contact with LEU 65 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29I THR* 4.6 4.7 - - + -
63I GLU* 4.1 1.8 - - + +
64I ILE* 1.3 89.1 - - - +
66I PRO* 1.3 77.8 - - + +
67I PRO* 3.7 4.7 - - - +
77I PRO* 3.7 21.5 - - + -
102I VAL* 5.6 0.3 - - - -
103I THR* 2.9 40.3 + - + +
105I GLN* 3.5 53.2 - - + +
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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