Contacts of the strand formed by residues 60 - 65 (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 HIS 60 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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51C LEU* 3.7 20.2 - - + +
55C ALA* 4.1 11.7 - - + +
56C LYS 4.0 11.4 - - - -
58C GLU* 2.9 46.8 + - - -
59C MET* 1.3 76.3 - - - +
61C ARG* 1.3 62.1 + - - +
62C VAL* 5.4 2.7 - - + -
82C SER* 3.2 5.0 - - - -
83C LEU* 2.8 40.8 + - + +
106C LEU* 4.1 4.3 - - + -
108C ALA 3.2 4.3 - - - +
109C GLY* 3.8 10.1 - - - -
110C SER 3.6 1.8 + - - -
111C GLY* 2.9 30.8 + - - -
113C VAL* 3.3 28.7 - - + -
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Residues in contact with ARG 61 (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* 5.6 1.3 - - - -
60C HIS* 1.3 76.1 - - - +
62C VAL* 1.3 63.3 - - - +
63C GLU* 3.3 17.8 + - - -
79C THR* 2.7 48.4 + - + +
81C ALA 3.3 11.9 - - - +
82C SER* 3.8 11.7 - - - +
106C LEU* 3.7 2.3 - - - +
107C ARG* 2.8 52.6 + - + +
108C ALA* 2.9 16.5 + - + +
51D LEU 4.5 2.7 - - - -
53D GLU* 2.8 43.7 + - - +
114D PHE* 3.5 33.9 - - - -
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Residues in contact with VAL 62 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23C LEU* 4.7 4.7 - - + -
49C ILE* 4.5 16.2 - - + -
60C HIS* 5.4 2.0 - - + -
61C ARG* 1.3 79.2 - - - +
63C GLU* 1.3 70.7 + - - +
79C THR* 3.8 3.6 - - - +
80C ILE* 3.0 46.9 + - + +
81C ALA* 2.9 19.1 + - + +
83C LEU* 6.1 1.8 - - + -
104C PHE* 4.6 3.1 - - + -
105C GLN 3.4 9.4 - - - +
106C LEU* 4.0 18.2 - - + -
113C VAL* 4.4 15.3 - - + -
115C LEU* 4.5 15.9 - - + -
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Residues in contact with GLU 63 (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* 3.3 18.0 + - - +
62C VAL* 1.3 81.3 - - - +
64C ILE* 1.3 62.3 + - - +
65C LEU* 3.6 8.2 - - + +
77C PRO* 3.5 29.1 - - + +
78C VAL 3.1 9.9 - - - +
79C THR* 3.9 15.2 + - - +
80C ILE* 4.4 0.9 - - - +
104C PHE* 3.4 4.5 - - - -
105C GLN* 2.8 35.8 + - - +
107C ARG* 2.9 55.5 + - + +
114D PHE* 5.8 0.3 - - - -
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Residues in contact with ILE 64 (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* 5.4 0.2 - - + -
63C GLU* 1.3 76.3 - - - +
65C LEU* 1.3 71.6 + - - +
66C PRO* 4.0 0.7 - - - +
77C PRO* 3.5 2.3 - - - +
78C VAL* 2.8 38.5 + - + +
80C ILE* 3.7 36.5 - - + +
98C LEU* 3.7 34.1 - - + -
102C VAL* 5.1 7.4 - - + -
103C THR 3.3 14.8 - - - +
104C PHE* 3.9 11.7 - - + -
18D LEU* 3.1 39.6 - - + +
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Residues in contact with LEU 65 (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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29C THR* 4.5 2.5 - - + -
63C GLU* 3.6 24.7 - - + +
64C ILE* 1.3 80.2 - - - +
66C PRO* 1.4 76.5 - - + +
67C PRO* 3.5 2.6 - - - +
77C PRO* 3.7 19.3 - - + -
103C THR* 2.9 42.5 + - + +
105C GLN* 3.4 40.8 - - + +
107C ARG* 4.2 6.5 - - - +
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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