Contacts of the strand formed by residues 49 - 58 (chain B) in PDB entry 2PZX
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 LYS 49 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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41B PHE* 4.1 45.9 - - + -
43B ILE* 4.8 5.8 - - + +
48B SER* 1.3 84.0 - - - +
50B GLN* 1.3 60.8 + - - +
51B LYS* 3.9 13.0 + - - +
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Residues in contact with GLN 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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41B PHE* 3.0 4.4 - - - -
42B ARG* 3.0 52.8 + - + +
44B LEU* 3.5 41.1 - - + +
48B SER 4.0 1.4 - - - -
49B LYS* 1.3 73.0 - - - +
51B LYS* 1.3 77.4 + - + +
52B VAL* 3.7 0.7 - - - +
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Residues in contact with LYS 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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40B ASP* 3.2 15.0 - - + +
41B PHE* 4.5 0.7 - - - +
42B ARG* 4.6 2.9 + - - -
49B LYS 4.5 10.3 + - - +
50B GLN* 1.3 86.8 - - + +
52B VAL* 1.3 70.5 + - - +
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Residues in contact with VAL 52 (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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40B ASP* 2.4 41.9 + - - +
41B PHE 4.3 2.9 - - - -
42B ARG* 3.3 57.2 - - + +
50B GLN 3.7 2.0 - - - +
51B LYS* 1.3 83.5 - - - +
53B ALA* 1.3 90.7 + - + +
54B ARG* 3.5 1.7 + - - -
55B HIS* 4.2 17.0 - - + +
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Residues in contact with ALA 53 (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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39B TYR 2.9 8.5 - - - +
52B VAL* 1.3 89.8 - - + +
54B ARG* 1.3 56.0 + - - +
55B HIS* 2.5 24.5 + - + +
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Residues in contact with ARG 54 (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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38B GLU* 2.7 53.4 + - - +
39B TYR 3.3 6.2 - - - +
40B ASP* 4.0 32.1 + - - +
52B VAL 3.5 2.3 + - - -
53B ALA* 1.3 69.1 - - - +
55B HIS* 1.3 58.5 + - - +
56B ILE 4.0 0.9 + - - -
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Residues in contact with HIS 55 (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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7B TYR* 4.9 2.2 - - - -
12B ASP* 3.2 35.1 + - - +
14B SER* 4.7 10.8 - - - +
38B GLU* 4.5 0.7 - - - -
39B TYR* 3.0 34.2 + - + +
41B PHE 4.6 8.5 - - - -
42B ARG* 5.7 1.6 - - + -
52B VAL* 4.2 13.9 - - + +
53B ALA* 2.5 22.1 + - + +
54B ARG* 1.3 72.9 - - - +
56B ILE* 1.3 60.0 + - - +
57B ARG* 2.8 53.8 + - + +
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Residues in contact with ILE 56 (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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13B ILE* 3.2 31.9 + - + +
14B SER* 3.5 27.0 + - - +
24B TYR* 4.4 22.0 - - + +
36B THR* 3.7 10.5 - - - +
37B GLY* 3.0 50.9 - - - +
38B GLU* 3.7 10.2 - - + +
54B ARG 4.0 2.0 + - - -
55B HIS* 1.3 75.3 - - - +
57B ARG* 1.3 65.8 + - - +
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Residues in contact with ARG 57 (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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2B ILE* 4.1 2.5 - - - -
7B TYR* 3.5 27.4 + - - -
10B THR* 2.6 52.4 + - - -
11B VAL* 3.1 16.9 - - - +
12B ASP 3.7 2.6 - - - +
13B ILE* 3.2 15.8 - - - +
36B THR* 3.4 1.6 - - - -
37B GLY 2.6 29.3 + - - -
39B TYR* 3.2 40.6 - - + -
55B HIS* 2.8 55.9 + - + +
56B ILE* 1.3 72.3 - - - +
58B GLY* 1.3 60.3 + - - +
121B ASP* 3.0 31.1 + - - -
122B LEU* 4.5 2.0 - - - +
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Residues in contact with GLY 58 (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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2B ILE* 4.5 1.1 - - - -
10B THR* 3.2 3.7 - - - -
11B VAL* 2.7 35.7 + - - +
13B ILE* 3.8 17.4 - - - +
31B VAL* 4.5 5.8 - - - -
35B LEU 4.5 2.2 - - - -
57B ARG* 1.3 78.0 - - - +
59B CYS* 1.3 53.6 + - - -
60B VAL* 2.7 28.6 + - - +
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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