Contacts of the strand formed by residues 60 - 68 (chain C) in PDB entry 4CYM
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 60 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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57C THR* 4.4 0.7 - - - -
58C ILE 2.9 9.5 + - - +
59C GLY* 1.3 77.1 - - - +
61C ASP* 1.3 75.9 + - - +
62C PHE* 3.6 27.7 - - + -
80C TRP* 4.5 9.6 - - + -
81C ASP 3.5 10.3 - - - +
82C ILE* 4.5 7.0 - - + -
95C TYR* 3.2 51.6 - - + +
509F GLN* 3.0 33.5 + - - +
513F LEU* 4.8 1.3 - - + -
543F ASP* 5.4 0.5 - - - +
546F LYS* 5.7 0.7 - - - +
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Residues in contact with ASP 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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39C THR* 5.0 7.4 - - - +
57C THR* 4.1 13.1 + - + +
60C VAL* 1.3 80.0 - - - +
62C PHE* 1.3 77.2 + - - +
80C TRP 3.6 0.3 - - - -
81C ASP* 2.7 59.8 + - + +
546F LYS* 2.9 31.1 + - - +
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Residues in contact with PHE 62 (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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42C ILE* 5.6 0.4 - - - -
60C VAL* 3.6 30.3 - - + -
61C ASP* 1.3 93.9 + - - +
63C ALA* 1.3 64.3 + - - +
79C LEU 3.2 5.4 - - - +
80C TRP* 3.6 52.3 - + - -
81C ASP* 5.6 1.3 - - - -
509F GLN* 4.0 6.7 - - - -
513F LEU* 4.8 5.6 - - + -
546F LYS* 3.5 28.9 - - + -
547F ALA* 3.9 30.1 - - + -
550F TYR* 3.5 45.4 + + + -
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Residues in contact with ALA 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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42C ILE* 3.7 29.4 - - + +
46C VAL* 4.5 15.5 - - + -
47C HIS* 5.2 6.7 - - + -
62C PHE* 1.3 76.7 - - - +
64C LEU* 1.3 60.1 + - - +
77C LEU 3.5 0.3 - - - +
78C GLN* 3.7 1.2 - - - -
79C LEU* 2.7 43.7 + - + +
550F TYR* 3.7 10.1 - - - -
586F GLN* 5.9 2.7 - - - +
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Residues in contact with LEU 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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25C LEU* 4.9 2.2 - - + -
46C VAL* 3.8 18.7 - - - +
63C ALA* 1.3 75.0 - - - +
65C LYS* 1.3 62.7 + - - +
66C VAL* 4.2 21.2 + - + +
76C ARG* 4.2 30.5 - - + +
77C LEU 3.3 19.1 - - - +
78C GLN* 4.5 12.1 - - + +
550F TYR* 3.5 16.6 + - + +
586F GLN* 3.3 36.8 + - + +
587F ASN* 3.6 22.2 - - - +
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Residues in contact with LYS 65 (chain C).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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45C TYR* 3.0 66.0 + - + +
46C VAL* 4.2 19.6 + - + +
48C GLN* 5.4 1.8 - - - +
64C LEU* 1.3 75.3 - - - +
66C VAL* 1.3 67.8 + - - +
67C LEU* 3.7 25.4 - - + -
75C VAL 3.4 2.4 - - - +
76C ARG* 3.5 1.7 - - - -
77C LEU* 2.6 55.2 + - + +
79C LEU* 4.6 4.0 - - + -
182C GLU* 4.6 7.0 + - - -
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Residues in contact with VAL 66 (chain C).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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64C LEU* 4.2 23.3 - - + +
65C LYS* 1.3 84.6 - - - +
67C LEU* 1.3 71.6 + - - +
68C ASN* 4.3 1.1 - - - +
74C LEU* 4.0 25.4 - - + -
75C VAL 3.5 4.3 - - - +
76C ARG* 4.6 24.2 - - + +
586F GLN 5.7 0.4 - - - +
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Residues in contact with LEU 67 (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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45C TYR* 3.8 16.2 - - + +
65C LYS* 3.7 32.8 - - + +
66C VAL* 1.3 77.6 - - - +
68C ASN* 1.3 65.1 + - - +
69C TRP* 3.4 21.4 + - + +
74C LEU* 3.2 11.0 - - - +
75C VAL* 2.9 50.3 + - + +
77C LEU* 4.7 6.7 - - + -
182C GLU* 5.7 2.2 - - - +
186C ARG* 6.0 5.4 - - - +
189C VAL* 4.3 22.9 - - + -
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Residues in contact with ASN 68 (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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66C VAL* 4.3 1.8 + - - +
67C LEU* 1.3 70.0 - - - +
69C TRP* 1.3 63.2 + - - +
70C ASP 3.8 10.2 - - - +
73C THR 4.4 2.2 - - - -
74C LEU* 3.7 22.0 - - - +
186C ARG* 5.1 5.5 + - - -
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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