Contacts of the strand formed by residues 42 - 49 (chain B) in PDB entry 4ZDH
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 GLY 42 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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104A ALA* 3.1 26.0 + - - +
36B ARG 3.6 1.2 - - - +
37B GLN* 3.4 16.7 - - - -
38B ASP 3.1 27.5 + - - -
40B GLY 3.7 1.2 - - - +
41B LEU* 1.3 84.0 - - - +
43B LEU* 1.3 59.1 + - - -
44B ARG* 3.9 3.1 + - - +
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Residues in contact with LEU 43 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45A PRO* 4.8 4.5 - - + -
89A LEU* 4.2 11.3 - - + +
102A PHE* 3.9 45.7 - - + +
103A GLY 4.9 5.3 + - - +
104A ALA* 4.5 5.8 + - - +
35B TYR* 3.6 32.5 - - + -
36B ARG 3.4 2.9 - - - +
37B GLN* 3.9 24.2 - - + +
41B LEU 4.0 2.6 - - - +
42B GLY* 1.3 71.8 - - - -
44B ARG* 1.3 63.7 + - - +
90B LEU* 3.8 25.8 - - + -
104B PHE* 4.1 20.9 - - + -
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Residues in contact with ARG 44 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35B TYR* 3.2 8.3 - - - -
36B ARG* 3.0 51.0 + - - +
38B ASP* 3.1 26.1 + - - -
41B LEU* 3.6 49.3 - - - +
42B GLY 4.2 2.1 + - - +
43B LEU* 1.3 80.7 - - - +
45B LEU* 1.3 61.6 + - - +
46B ILE 3.5 0.7 + - - -
59B ASP* 5.1 5.6 - - + -
60B ILE* 3.7 43.8 - - + +
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Residues in contact with LEU 45 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99A LYS* 3.6 34.1 - - + +
100A LEU 5.1 5.6 - - - +
33B PHE* 4.0 14.1 - - + -
34B TRP 3.4 16.4 - - - +
35B TYR* 3.6 31.4 - - + +
44B ARG* 1.3 71.1 - - - +
46B ILE* 1.3 56.3 - - - +
47B TYR 3.5 15.3 - - - +
48B PHE* 3.7 17.9 - - + -
58B GLY* 4.1 11.4 - - - -
59B ASP* 2.7 46.7 + - - +
60B ILE* 3.0 10.8 + - - +
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Residues in contact with ILE 46 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34B TRP* 2.8 14.2 + - + +
35B TYR* 4.0 3.6 - - - +
36B ARG* 4.0 17.7 - - + +
45B LEU* 1.3 72.8 - - - +
47B TYR* 1.3 74.4 + - + +
58B GLY* 2.8 22.7 + - - -
60B ILE* 3.9 26.7 - - + +
61B PRO* 3.6 8.4 - - + +
64B TYR* 3.6 44.2 - - + -
76B LEU* 4.0 16.8 - - + -
89B TYR* 3.8 34.3 - - + -
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Residues in contact with TYR 47 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34B TRP* 2.9 28.6 + - + -
45B LEU* 3.5 5.4 - - - +
46B ILE* 1.3 101.1 - - + +
48B PHE* 1.3 64.1 + - - +
55B LYS* 4.4 16.9 + - + -
56B GLU* 3.3 23.8 - - - -
57B LYS* 3.3 41.7 + - + +
58B GLY* 3.7 2.4 - - - +
61B PRO* 3.8 13.9 - - + -
64B TYR* 3.8 23.4 + - + -
65B SER* 4.1 9.7 - - - -
66B VAL* 3.4 47.1 - - + -
74B PHE* 3.9 3.3 - - + -
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Residues in contact with PHE 48 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99A LYS* 3.9 28.7 - - + -
32B MET 3.3 6.5 - - - -
33B PHE* 3.5 29.2 - + + -
45B LEU* 3.7 19.1 - - + -
47B TYR* 1.3 76.2 - - - +
49B SER* 1.3 65.8 + - - +
50B TYR* 3.3 48.2 - + - -
55B LYS* 3.4 2.9 - - - +
56B GLU* 2.9 65.7 + - + -
57B LYS 3.7 11.9 - - - -
58B GLY* 4.3 1.3 - - - -
74B PHE* 3.7 6.2 - - - -
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Residues in contact with SER 49 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31B ASN* 3.3 6.4 - - - +
32B MET 2.9 32.3 + - - +
33B PHE* 5.4 0.2 - - - -
48B PHE* 1.3 79.5 - - - +
50B TYR* 1.3 64.2 + - - +
51B ASP 2.8 8.7 + - - -
54B MET 2.7 27.2 + - - -
55B LYS* 4.4 2.0 - - - +
56B GLU* 4.9 0.9 - - - +
68B ARG* 2.5 31.8 + - - -
74B PHE* 3.8 19.1 - - - -
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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