Contacts of the strand formed by residues 36 - 42 (chain M) in PDB entry 2ZQK
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 ALA 36 (chain M).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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28M VAL* 3.0 34.7 - - + +
30M ILE* 3.7 21.3 - - + +
34M GLY 3.2 7.2 + - - +
35M ASN* 1.3 67.7 - - - +
37M ILE* 1.3 60.1 + - - +
38M PRO* 3.8 0.2 - - - +
36N ALA 3.3 16.6 + - - +
37N ILE* 3.6 17.2 - - + -
38N PRO* 3.6 10.4 - - + +
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Residues in contact with ILE 37 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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172A LEU* 6.1 2.5 - - + -
28M VAL* 3.5 1.1 - - - -
29M ASN* 2.7 50.6 + - + +
31M ASP* 4.6 5.8 - - + +
35M ASN* 3.0 24.6 + - + +
36M ALA* 1.3 72.2 - - - +
38M PRO* 1.3 76.8 - - + +
39M SER 3.2 0.2 + - - -
23N PRO* 5.7 4.9 - - + -
28N VAL* 5.5 2.7 - - + -
36N ALA* 4.7 8.7 - - + -
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Residues in contact with PRO 38 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26M GLN* 3.0 28.7 - - - +
27M LYS 4.2 0.9 - - - +
28M VAL* 3.9 8.7 - - + -
36M ALA 3.6 6.2 - - - +
37M ILE* 1.3 89.0 - - + +
39M SER* 1.3 59.3 + - - +
40M GLY 4.7 0.4 - - - +
23N PRO* 3.0 45.0 - - + +
26N GLN* 3.7 18.6 - - + +
28N VAL* 3.9 26.7 - - + -
38N PRO* 3.9 13.0 - - + -
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Residues in contact with SER 39 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27M LYS* 2.9 39.4 + - - +
28M VAL 4.3 1.8 - - - -
29M ASN* 3.6 29.6 - - - -
37M ILE 3.2 2.6 + - - -
38M PRO* 1.3 73.5 - - - +
40M GLY* 1.3 60.9 + - - +
41M VAL* 3.4 15.0 + - - +
21N GLN 4.3 1.0 - - - +
23N PRO* 3.1 16.9 - - - +
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Residues in contact with GLY 40 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20M PHE* 3.6 21.6 - - - -
26M GLN* 4.3 5.7 - - - +
27M LYS 4.5 0.2 + - - -
38M PRO 3.4 3.2 - - - -
39M SER* 1.3 78.5 - - - +
41M VAL* 1.3 64.5 + - - +
20N PHE 3.6 20.2 - - - -
21N GLN* 3.7 26.5 - - - +
23N PRO* 4.3 2.7 - - - -
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Residues in contact with VAL 41 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20M PHE* 4.6 2.4 - - - -
26M GLN* 3.8 3.4 - - - +
27M LYS* 2.7 53.3 + - + +
39M SER* 3.4 15.2 - - - +
40M GLY* 1.3 87.2 - - - +
42M LEU* 1.3 69.0 + - - +
44M ASP* 5.6 0.7 - - - +
47M VAL* 5.7 2.7 - - + -
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Residues in contact with LEU 42 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16M THR* 3.9 19.3 - - + +
19M ALA* 4.2 2.5 - - + +
20M PHE* 3.2 56.5 - - + +
25M ASN* 3.3 30.1 - - + +
26M GLN* 4.6 2.0 - - - -
27M LYS* 3.7 6.4 - - - +
41M VAL* 1.3 88.4 - - - +
43M LYS* 1.3 66.7 + - - +
44M ASP* 3.3 3.6 + - - +
46M VAL* 4.3 6.5 - - + -
47M VAL* 3.8 24.7 - - + +
50M ILE* 4.2 20.9 - - + -
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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