Contacts of the strand formed by residues 63 - 68 (chain D) in PDB entry 5BRZ
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 LEU 63 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48D LEU* 4.1 34.8 - - + +
49D LEU* 4.2 13.0 - - + -
59D THR* 3.3 2.9 + - - -
60D SER* 3.0 46.5 + - - +
61D GLY 3.3 1.9 - - - +
62D ARG* 1.3 82.9 - - + +
64D ASN* 1.3 70.4 + - - +
76D LEU* 4.0 14.6 - - + -
77D TYR 3.1 5.8 - - - +
78D ILE* 3.7 34.8 - - + -
89D TYR* 5.6 2.7 - - + +
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Residues in contact with ASN 64 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49D LEU* 3.8 4.0 - - - -
57D GLU* 3.5 36.8 + - - +
58D GLN 3.4 7.4 + - - -
59D THR* 2.9 22.8 + - - -
63D LEU* 1.3 78.0 - - - +
65D ALA* 1.3 61.9 + - - +
75D THR 3.4 0.5 - - - +
76D LEU* 3.2 6.8 - - - +
77D TYR* 2.6 59.4 + - + -
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Residues in contact with ALA 65 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36D TRP* 4.5 12.6 - - + -
49D LEU* 3.6 20.3 - - + +
51D VAL* 5.3 10.8 - - + -
57D GLU* 3.5 23.0 - - - +
58D GLN* 2.9 20.9 + - + +
64D ASN* 1.3 79.5 + - - +
66D SER* 1.3 64.0 + - - +
74D SER* 4.3 8.7 - - - +
75D THR 3.1 9.6 - - - +
76D LEU* 4.7 0.2 - - + -
77D TYR* 4.7 1.2 - - - -
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Residues in contact with SER 66 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51D VAL* 5.8 0.4 - - - -
56D ARG 3.2 12.8 - - - -
57D GLU* 5.6 1.3 - - - -
65D ALA* 1.3 78.0 - - - +
67D LEU* 1.3 62.0 + - - +
68D ASP 4.3 0.2 - - - -
73D ARG 5.3 0.2 + - - -
74D SER* 2.8 26.2 + - - -
75D THR* 2.8 33.9 + - - +
77D TYR* 4.1 12.0 + - - -
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Residues in contact with LEU 67 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26D PHE* 4.3 12.8 - - + -
31D ILE* 4.4 7.4 - - + -
34D LEU* 3.3 40.8 - - + -
51D VAL* 4.3 16.6 - - + -
52D ARG 4.4 7.4 - - - +
53D PRO* 4.0 12.3 - - + +
55D GLN 3.5 23.5 - - - +
56D ARG* 3.0 32.8 + - - +
66D SER* 1.3 75.9 - - - +
68D ASP* 1.3 63.1 + - - +
69D LYS* 3.7 24.6 + - + +
73D ARG 3.6 5.8 - - - +
74D SER* 4.5 0.9 - - - +
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Residues in contact with ASP 68 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26D PHE* 4.9 0.4 - - - -
56D ARG* 5.4 7.8 + - - +
67D LEU* 1.3 75.2 - - - +
69D LYS* 1.3 52.3 + - - +
70D SER* 2.9 24.8 + - - -
71D SER* 3.0 22.7 + - - +
72D GLY 2.6 30.0 + - - -
73D ARG* 2.9 25.5 + - + +
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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