Contacts of the strand formed by residues 46 - 51 (chain B) in PDB entry 1ZQ1
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 THR 46 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3B VAL* 3.3 19.2 - - - +
38B PRO* 5.7 5.2 - - - +
42B SER* 4.9 11.0 - - - +
44B GLY 2.4 32.1 + - - +
45B ASP* 1.3 82.5 - - - +
47B LEU* 1.3 68.7 + - - +
48B VAL* 4.2 3.7 + - - +
58B GLY* 4.1 0.9 - - - -
59B ILE 3.3 13.6 + - - -
60B ALA* 4.9 0.7 - - - -
61B LEU* 4.4 0.7 - - - +
117D ASP* 6.2 1.1 - - - -
118D GLU* 2.7 42.8 + - - +
120D TYR* 4.1 3.6 + - - +
442D ARG* 5.6 4.3 - - - -
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Residues in contact with LEU 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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3B VAL* 4.2 7.4 - - + -
6B PHE* 5.3 0.4 - - + -
7B LEU* 4.6 15.3 - - + -
35B ILE* 3.8 36.1 - - + -
36B MSE 4.8 2.9 - - - +
46B THR* 1.3 74.5 - - - +
48B VAL* 1.3 86.1 + - - +
49B LEU* 3.9 6.1 + - + -
57B ILE 3.6 0.2 - - - +
58B GLY* 3.4 2.3 - - - -
59B ILE* 2.7 57.6 + - + +
61B LEU* 3.8 19.7 - - + +
64B ILE* 5.0 12.1 - - + -
67B ILE* 5.3 10.3 - - + -
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Residues in contact with VAL 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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35B ILE* 3.9 0.9 - - - -
36B MSE 3.0 47.8 + - + +
37B PRO 4.1 15.9 - - - +
38B PRO* 4.7 9.4 - - + -
46B THR* 4.9 3.6 - - + +
47B LEU* 1.3 87.1 - - - +
49B LEU* 1.3 62.2 + - - +
56B ASN* 4.4 14.1 - - + +
57B ILE 3.1 11.0 - - - +
120D TYR* 3.0 49.1 - - + +
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Residues in contact with LEU 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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18B VAL* 5.0 6.1 - - + +
20B ILE* 5.6 7.2 - - + +
31B TYR* 3.6 31.2 - - + -
32B GLU 4.0 1.8 - - - +
33B GLY* 3.0 51.4 - - - +
34B TYR 3.5 10.3 - - - +
35B ILE* 3.9 12.8 - - + +
36B MSE 4.3 2.9 - - - -
47B LEU* 3.9 4.9 + - + -
48B VAL* 1.3 75.8 - - - +
50B LYS* 1.3 60.6 + - - +
51B LEU* 3.8 10.6 + - + -
55B TYR 3.6 1.4 - - - +
56B ASN* 3.4 2.7 - - - -
57B ILE* 2.8 42.3 + - + +
59B ILE* 4.9 13.0 - - + -
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Residues in contact with LYS 50 (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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33B GLY* 3.0 4.0 - - - -
34B TYR* 2.8 53.5 + - + +
36B MSE 3.4 23.8 - - + +
49B LEU* 1.3 73.3 - - - +
51B LEU* 1.3 67.6 + - - +
54B GLY* 3.4 27.6 + - - +
55B TYR 3.5 2.9 - - - -
56B ASN* 2.9 28.7 + - - +
109B TYR 4.3 7.6 + - - +
110B GLU* 4.4 14.1 - - - +
111B THR 3.3 29.3 + - - -
112B GLY* 3.7 8.5 - - - +
122D MET* 4.3 2.2 - - - +
432D MET 5.6 1.0 + - - -
434D PRO* 4.5 6.5 - - - +
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Residues in contact with LEU 51 (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 TYR* 4.6 9.6 - - + -
32B GLU 3.8 15.3 - - - +
34B TYR* 5.3 0.9 - - - -
49B LEU* 3.8 26.0 - - + +
50B LYS* 1.3 79.6 - - - +
52B GLU* 1.3 54.8 + - - +
53B ASN* 2.8 22.2 - - + +
54B GLY* 2.6 28.4 + - - -
55B TYR 3.0 8.9 + - - +
57B ILE* 3.2 44.9 - - + -
140D ILE* 3.5 22.0 - - + -
143D THR* 4.7 5.8 - - + -
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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