Contacts of the strand formed by residues 26 - 30 (chain N) 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 GLN 26 (chain N).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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174A GLY* 4.6 1.7 - - - +
26M GLN* 2.8 39.8 + - - +
38M PRO* 3.7 9.4 - - + +
20N PHE* 3.8 28.7 - - + +
22N ASN 3.9 2.6 + - - +
23N PRO* 3.6 18.5 + - - +
24N ASP 3.0 9.4 - - - +
25N ASN* 1.3 79.6 - - - +
27N LYS* 1.3 64.0 + - - +
28N VAL* 4.0 5.4 + - - +
38N PRO* 3.9 5.1 - - - +
39N SER 3.5 11.3 - - - +
40N GLY* 3.2 24.9 - - - +
41N VAL 3.2 17.3 - - - +
42N LEU* 4.1 5.4 - - + -
43N LYS* 4.2 6.1 - - - -
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Residues in contact with LYS 27 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158A SER 3.5 7.4 - - - -
159A GLY* 2.7 24.1 + - - +
160A VAL* 3.4 19.5 - - + -
174A GLY 3.7 5.2 - - - -
176A ASN* 3.9 28.7 + - + -
177A VAL* 4.3 4.8 - - - +
178A ASN* 6.1 0.2 - - - +
26N GLN* 1.3 82.1 + - - +
28N VAL* 1.3 62.0 + - - +
39N SER* 2.6 33.0 + - - +
41N VAL* 3.0 27.9 + - + +
42N LEU 4.0 5.4 - - - -
43N LYS* 3.9 19.1 - - + +
44N ASP* 2.8 28.0 + - - -
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Residues in contact with VAL 28 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172A LEU* 5.5 1.1 - - + -
173A PRO 5.1 3.8 - - - +
174A GLY 3.0 16.6 + - - +
175A VAL* 3.5 13.1 - - + +
176A ASN* 2.8 28.1 + - - +
37M ILE* 5.3 2.9 - - + -
38M PRO* 3.9 29.6 - - + -
23N PRO 6.0 0.2 - - - +
26N GLN 4.7 3.1 - - - +
27N LYS* 1.3 81.1 - - - +
29N ASN* 1.3 79.6 + - - +
30N ILE* 4.4 4.7 - - + -
36N ALA* 3.5 24.9 - - + -
37N ILE 3.6 7.2 - - - +
39N SER* 4.1 0.9 - - - -
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Residues in contact with ASN 29 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176A ASN* 3.3 30.8 + - - +
178A ASN 4.7 0.6 + - - +
179A THR* 3.3 20.0 - - - +
180A PRO* 4.9 6.9 - - + +
23M PRO* 5.6 2.0 - - - +
28N VAL* 1.3 89.6 - - - +
30N ILE* 1.3 72.2 + - - +
37N ILE* 2.9 39.6 + - + +
38N PRO 4.2 2.4 + - - -
39N SER* 3.6 25.9 + - - +
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Residues in contact with ILE 30 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146A THR* 3.8 12.8 - - + +
163A THR* 5.3 0.2 - - - +
172A LEU* 3.7 22.4 - - + -
175A VAL* 4.2 22.4 - - + -
179A THR* 2.8 14.0 + - + +
180A PRO* 3.4 11.1 - - - +
181A ASN* 3.1 38.2 - - - +
182A VAL* 4.3 7.0 - - + -
28N VAL* 4.4 4.0 - - + -
29N ASN* 1.3 91.3 - - - +
31N ASP* 1.3 71.4 + - - +
34N GLY* 3.6 20.9 - - - +
35N ASN 3.2 18.4 - - - +
36N ALA* 3.7 1.3 - - - -
37N ILE* 4.6 3.3 - - - +
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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
------------------------------------------------------------
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