Contacts of the strand formed by residues 55 - 60 (chain C) in PDB entry 3HU1
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 ASP 55 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50C GLN 4.8 1.7 - - - +
51C LEU* 4.1 13.1 - - + +
52C PHE* 3.2 47.7 + - - +
53C ARG 3.3 5.0 - - - +
54C GLY* 1.3 80.0 - - - +
56C THR* 1.3 67.3 + - - +
57C VAL 3.6 0.3 + - - -
70C ILE* 3.4 2.2 - - - -
71C VAL* 3.0 34.9 + - + +
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Residues in contact with THR 56 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54C GLY 3.9 0.8 + - - -
55C ASP* 1.3 75.9 - - - +
57C VAL* 1.3 62.2 + - - +
68C VAL* 6.0 1.8 - - - -
69C CYS 3.4 2.9 - - - +
70C ILE* 4.5 11.9 - - + -
104C PRO* 4.6 0.3 - - - +
105C CYS* 3.1 45.1 + - - +
106C PRO* 4.7 3.1 - - - +
108C VAL* 3.8 14.1 - - + +
143C TYR 5.8 0.4 - - - +
145C PRO* 3.7 32.5 - - + -
175C ILE* 4.4 21.7 - - + +
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Residues in contact with VAL 57 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39C VAL* 3.9 22.9 - - + -
51C LEU* 3.9 23.6 - - + -
55C ASP 4.1 0.7 - - - +
56C THR* 1.3 77.9 - - - +
58C LEU* 1.3 59.5 + - - +
59C LEU* 4.5 4.5 - - + -
67C ALA 3.8 0.2 - - - +
68C VAL* 3.3 9.0 - - - +
69C CYS* 2.7 52.8 + - + +
71C VAL* 3.8 27.4 - - + -
102C ILE* 4.1 14.8 - - + -
103C GLN 3.4 14.4 - - - +
105C CYS* 3.8 5.8 - - - -
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Residues in contact with LEU 58 (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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57C VAL* 1.3 73.2 - - - +
59C LEU* 1.3 73.1 + - - +
60C LYS* 4.2 9.0 - - + +
66C GLU* 3.8 39.9 - - + +
67C ALA 3.8 9.6 - - - +
68C VAL* 4.1 13.2 - - + -
101C SER 4.0 0.5 - - - +
102C ILE* 3.6 2.6 - - - -
103C GLN* 2.7 71.7 + - + +
104C PRO 4.8 0.2 - - - +
105C CYS* 3.7 15.3 - - + +
147C ARG* 5.5 0.2 - - - -
173C TYR* 4.5 21.5 - - + +
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Residues in contact with LEU 59 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39C VAL* 3.8 13.7 - - + -
57C VAL* 4.5 8.1 - - + -
58C LEU* 1.3 74.5 - - - +
60C LYS* 1.3 61.1 + - - +
66C GLU* 3.3 11.1 - - - +
67C ALA* 2.9 36.3 + - + +
69C CYS* 3.7 29.6 - - + -
82C ILE* 3.8 14.1 - - + -
84C MET* 4.1 3.4 - - + -
88C VAL* 4.1 2.7 - - + -
92C LEU* 3.9 28.5 - - + -
100C ILE* 3.9 5.6 - - + -
101C SER 3.4 9.9 - - - +
102C ILE* 3.7 36.1 - - + -
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Residues in contact with LYS 60 (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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433B GLU* 4.9 10.7 + - + -
58C LEU* 4.2 9.0 - - + +
59C LEU* 1.3 78.3 - - - +
61C GLY* 1.3 62.9 + - - +
65C ARG 3.6 5.2 - - - +
66C GLU* 3.8 28.0 - - + +
92C LEU* 4.1 2.2 - - - -
100C ILE* 3.4 9.5 - - - +
101C SER* 3.2 45.8 + - - +
103C GLN* 3.0 40.1 + - + +
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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
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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