Contacts of the strand formed by residues 54 - 59 (chain D) in PDB entry 2ZHX
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 ASN 54 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92C ARG* 2.9 31.2 - - - +
96C ASN* 5.2 4.9 + - - +
194C PRO* 3.3 21.7 - - + +
45D THR* 4.6 3.1 - - + -
46D ALA 3.8 3.1 - - - -
47D TYR* 3.6 9.5 - - - -
52D ASP 4.4 0.8 + - - +
53D GLU* 1.3 72.3 - - - +
55D VAL* 1.3 61.1 + - - +
56D MET* 3.8 10.2 - - + +
71D VAL 3.6 1.4 - - - +
72D ILE* 3.5 4.5 - - - +
73D GLN* 2.9 63.1 + - + +
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Residues in contact with VAL 55 (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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8D ILE* 4.0 33.1 - - + +
12D THR* 5.1 3.4 - - + +
14D LYS* 6.0 2.2 - - + -
16D LEU* 3.7 25.1 - - + -
44D HIS 3.8 0.7 - - - +
45D THR* 3.5 1.6 - - - -
46D ALA* 2.8 44.2 + - + +
48D ASP* 4.5 7.4 - - + +
53D GLU* 4.3 15.5 - - + +
54D ASN* 1.3 77.8 - - - +
56D MET* 1.3 64.1 + - - +
57D LEU 4.1 0.2 + - - -
70D LEU* 4.0 19.5 - - + -
71D VAL 3.8 1.6 - - - +
72D ILE* 4.7 14.1 - - + -
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Residues in contact with MET 56 (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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194C PRO* 3.7 10.8 - - + -
195C LEU* 3.7 39.0 - - - -
43D VAL* 4.4 3.6 - - + -
44D HIS 3.3 3.4 - - - +
45D THR* 3.7 24.5 - - + +
54D ASN* 3.8 15.3 - - + +
55D VAL* 1.3 77.8 - - - +
57D LEU* 1.3 60.6 + - - +
58D LEU* 4.0 15.5 - - + -
69D ALA 4.0 0.2 - - - +
70D LEU* 3.3 10.3 - - - +
71D VAL* 2.8 57.7 + - + +
73D GLN* 3.6 36.6 - - + +
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Residues in contact with LEU 57 (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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4D LEU* 3.7 21.5 - - + -
7D ILE* 3.4 34.1 - - + -
8D ILE* 3.9 26.8 - - + +
44D HIS* 2.8 49.5 + - + +
55D VAL 4.1 0.6 + - - -
56D MET* 1.3 73.4 - - - +
58D LEU* 1.3 67.6 + - - +
59D THR* 3.9 12.1 - - + -
67D PRO* 4.8 1.3 - - + -
69D ALA 3.1 22.9 - - - +
70D LEU* 4.4 6.7 - - + -
84D LEU* 4.1 17.5 - - + -
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Residues in contact with LEU 58 (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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195C LEU* 3.8 15.5 - - + -
29D VAL* 3.7 18.6 - - + -
33D ILE* 3.2 29.6 - - + -
41D ILE* 3.8 12.8 - - + -
42D LEU 3.3 3.8 - - - -
43D VAL* 4.0 19.1 - - + -
56D MET* 4.0 24.9 - - + +
57D LEU* 1.3 78.6 - - - +
59D THR* 1.3 63.4 + - - +
68D TRP* 2.9 36.0 + - + -
69D ALA* 2.9 16.4 + - + +
71D VAL* 4.1 17.0 - - + -
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Residues in contact with THR 59 (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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4D LEU* 4.7 4.5 - - + -
41D ILE* 3.3 14.8 - - - +
42D LEU* 2.9 28.0 + - - +
44D HIS* 3.1 33.9 - - + +
57D LEU* 3.9 17.7 - - + -
58D LEU* 1.3 81.2 - - - +
60D SER* 1.3 71.5 + - - +
65D TYR* 4.1 10.2 - - - +
66D LYS 3.0 22.0 - - - +
67D PRO* 3.9 8.3 - - + -
68D TRP* 4.3 5.4 - - - +
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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