Contacts of the strand formed by residues 66 - 72 (chain D) in PDB entry 5B6N
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 66 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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29D LEU* 6.4 0.2 - - - -
33D TRP* 3.5 14.6 - - + -
35D ILE* 3.6 21.5 - - + -
58D ALA 5.5 0.2 - - - +
61D PHE* 3.0 54.0 - - + +
62D ALA* 4.4 10.6 + - - +
64D ARG* 2.4 24.0 + - + +
65D ASN* 1.3 75.7 - - - +
67D LYS* 1.3 60.3 + - - +
68D LEU* 4.8 0.6 - - - +
164D VAL* 4.1 10.5 - - + -
168D GLN* 3.6 23.6 - - - +
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Residues in contact with LYS 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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25D PHE* 3.4 33.8 - - + -
28D PHE* 2.4 56.9 + - + -
29D LEU* 3.7 30.4 + - + +
32D SER* 5.3 0.4 - - - -
33D TRP 3.4 13.1 + - - +
34D GLY* 4.4 3.0 - - - -
35D ILE* 3.0 26.2 + - - +
66D VAL* 1.3 75.5 - - - +
68D LEU* 1.3 72.4 + - - +
69D ILE* 5.3 1.8 - - + -
101D PRO* 6.0 0.4 - - + -
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Residues in contact with LEU 68 (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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35D ILE* 3.4 22.4 - - + +
37D PHE* 4.9 8.5 - - + -
54D ALA* 4.0 28.5 - - + +
57D LEU* 5.0 0.2 - - + -
58D ALA* 4.4 12.7 - - + +
61D PHE* 3.7 55.4 - - + -
67D LYS* 1.3 89.3 - - - +
69D ILE* 1.3 66.6 + - - +
100D PHE* 3.6 22.5 - - + +
101D PRO* 3.5 19.4 - - - +
157D PHE* 5.3 3.8 - - + -
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Residues in contact with ILE 69 (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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25D PHE* 4.6 19.5 - - + -
28D PHE* 4.7 12.1 - - + -
35D ILE 3.2 14.7 + - - +
36D LEU* 3.4 28.7 - - + +
37D PHE* 2.8 34.6 + - - +
67D LYS* 5.1 2.9 - - + +
68D LEU* 1.3 79.7 - - - +
70D ALA* 1.3 83.2 + - - +
71D LEU* 3.9 0.2 - - + -
100D PHE* 4.6 1.5 - - - +
101D PRO* 3.7 28.7 - - + -
103D ILE* 3.7 28.0 - - + -
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Residues in contact with ALA 70 (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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37D PHE* 3.1 30.5 - - + -
39D HIS* 3.9 15.7 - - + -
51D LEU* 4.2 4.7 - - + -
69D ILE* 1.3 82.4 - - - +
71D LEU* 1.3 63.6 + - - +
100D PHE* 4.5 2.2 - - + -
101D PRO 3.2 17.0 + - - +
102D ILE* 4.0 11.4 - - + -
103D ILE 3.1 23.2 + - - -
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Residues in contact with LEU 71 (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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36D LEU* 3.6 23.6 - - + -
37D PHE 3.0 7.1 + - - +
38D SER* 4.1 16.4 - - - +
39D HIS* 2.8 34.7 + - - -
70D ALA* 1.3 82.4 - - - +
72D SER* 1.3 63.4 + - - +
103D ILE* 3.6 36.8 - - + -
105D ASP* 3.2 30.7 - - + +
110D LEU* 4.9 6.7 - - + -
116D MET* 3.7 30.1 - - + -
130D THR* 5.9 1.1 - - + -
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Residues in contact with SER 72 (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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39D HIS* 3.3 27.0 + - - -
41D ARG* 3.6 22.5 - - - -
42D ASP* 3.8 9.7 + - - -
71D LEU* 1.3 79.6 - - - +
73D ILE* 1.3 70.1 + - - +
74D ASP 3.7 0.9 - - - -
79D HIS* 3.4 18.8 - - - -
103D ILE 3.9 4.4 + - - -
105D ASP* 2.9 31.2 + - - +
130D THR* 4.1 7.2 - - - -
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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