Contacts of the strand formed by residues 60 - 68 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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57A THR* 4.4 1.6 - - - -
58A ILE 3.0 8.8 + - - +
59A GLY* 1.3 75.7 - - - +
61A ASP* 1.3 75.0 + - - +
62A PHE* 3.7 26.5 - - + -
80A TRP* 4.4 9.4 - - + -
81A ASP 3.5 11.9 - - - +
82A ILE* 4.5 6.7 - - + -
95A TYR* 3.3 50.9 - - + +
509D GLN* 2.9 38.3 + - - +
513D LEU* 4.8 1.3 - - + -
543D ASP* 5.2 1.4 - - - +
546D LYS* 5.6 1.4 - - - +
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Residues in contact with ASP 61 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39A THR* 4.9 8.0 - - - +
57A THR* 4.1 12.5 + - + +
60A VAL* 1.3 79.1 - - - +
62A PHE* 1.3 77.3 + - - +
80A TRP 3.6 0.5 - - - -
81A ASP* 2.7 60.4 + - + +
546D LYS* 2.8 30.9 + - - +
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Residues in contact with PHE 62 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42A ILE* 5.7 0.4 - - - -
60A VAL* 3.7 28.7 - - + -
61A ASP* 1.3 92.4 + - - +
63A ALA* 1.3 63.6 + - - +
79A LEU 3.2 5.8 - - - -
80A TRP* 3.5 53.6 - + - -
81A ASP* 5.6 1.3 - - - -
509D GLN* 4.1 6.5 - - - -
513D LEU* 4.8 5.6 - - + -
546D LYS* 3.4 28.4 + - + -
547D ALA* 3.7 31.0 - - + -
550D TYR* 3.5 44.1 + + + -
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Residues in contact with ALA 63 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42A ILE* 3.7 28.9 - - + +
46A VAL* 4.4 15.3 - - + -
47A HIS* 5.2 6.7 - - + -
62A PHE* 1.3 78.0 - - - +
64A LEU* 1.3 59.3 + - - +
77A LEU 3.5 0.3 - - - +
78A GLN* 3.7 1.6 - - - -
79A LEU* 2.7 44.1 + - + +
550D TYR* 3.8 10.6 - - - -
586D GLN* 6.0 2.5 - - - +
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Residues in contact with LEU 64 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25A LEU* 4.9 2.9 - - + -
46A VAL* 3.8 17.7 - - - +
63A ALA* 1.3 73.7 - - - +
65A LYS* 1.3 60.8 - - - +
66A VAL* 4.2 21.0 + - + +
76A ARG* 4.2 31.4 - - + +
77A LEU 3.3 19.3 - - - +
78A GLN* 4.5 12.1 - - + +
550D TYR* 3.7 15.7 + - + +
586D GLN* 3.5 34.6 + - + +
587D ASN* 3.9 19.3 - - - +
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Residues in contact with LYS 65 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45A TYR* 3.0 64.1 + - + +
46A VAL* 4.2 19.6 + - + +
48A GLN* 5.8 4.0 - - - +
64A LEU* 1.3 75.7 - - - +
66A VAL* 1.3 71.5 + - - +
67A LEU* 3.2 23.3 - - + -
75A VAL 3.5 1.7 - - - +
76A ARG* 3.5 1.7 - - - -
77A LEU* 2.6 53.3 + - + +
79A LEU* 4.6 3.6 - - + -
182A GLU* 4.5 7.4 + - - -
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Residues in contact with VAL 66 (chain A).
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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64A LEU* 4.2 22.4 + - + +
65A LYS* 1.3 87.4 + - - +
67A LEU* 1.3 69.9 + - - +
68A ASN* 4.4 1.1 + - - +
74A LEU* 4.0 25.4 - - + -
75A VAL 3.5 4.3 - - - +
76A ARG* 4.5 26.2 - - + +
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Residues in contact with LEU 67 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45A TYR* 3.8 16.6 - - - +
65A LYS* 3.2 38.8 - - + +
66A VAL* 1.3 77.8 - - - +
68A ASN* 1.3 63.8 + - - +
69A TRP* 3.4 27.3 + - + +
74A LEU* 3.2 11.0 - - - +
75A VAL* 2.9 58.7 + - + +
77A LEU* 4.5 4.3 - - + -
185A ALA* 5.9 0.7 - - + -
186A ARG* 5.4 5.8 - - + -
189A VAL* 4.5 10.5 - - + -
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Residues in contact with ASN 68 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66A VAL* 4.4 1.3 + - - +
67A LEU* 1.3 69.4 - - - +
69A TRP* 1.3 64.6 + - - +
70A ASP 3.7 10.4 - - - +
73A THR 4.4 2.2 - - - -
74A LEU* 3.7 22.0 - - - +
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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