Contacts of the strand formed by residues 26 - 30 (chain D) 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 D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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174B GLY 5.0 1.7 - - - +
26C GLN* 2.7 39.7 + - - +
38C PRO* 3.2 16.9 - - + +
19D ALA 5.2 0.2 + - - -
20D PHE* 3.8 30.8 - - + +
22D ASN 3.8 3.6 + - - +
23D PRO* 4.0 15.5 - - - +
24D ASP 3.3 9.5 - - - +
25D ASN* 1.3 84.4 - - - +
27D LYS* 1.3 68.8 + - - +
28D VAL* 5.7 0.8 - - - +
38D PRO* 3.6 10.9 - - - +
39D SER 3.7 2.4 - - - +
40D GLY* 3.1 26.8 - - - +
41D VAL 3.5 13.0 - - - +
42D LEU* 4.0 4.9 - - + +
43D LYS* 4.1 9.0 + - - -
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Residues in contact with LYS 27 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158B SER 3.2 23.1 - - - -
159B GLY* 3.3 16.4 + - - -
160B VAL* 3.7 16.6 - - + -
174B GLY 4.4 3.6 - - - -
176B ASN* 3.5 28.7 + - + +
177B VAL* 4.7 3.6 - - - +
26D GLN* 1.3 83.5 + - - +
28D VAL* 1.3 64.4 + - - +
38D PRO* 4.2 0.3 - - - +
39D SER* 2.5 38.3 + - - +
41D VAL* 2.7 25.7 + - + +
42D LEU 3.5 23.8 + - - +
43D LYS* 3.9 2.9 - - + +
44D ASP* 3.2 16.5 + - - -
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Residues in contact with VAL 28 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172B LEU* 5.7 0.2 - - + -
173B PRO 5.1 4.0 - - - +
174B GLY 3.4 17.3 + - - +
175B VAL* 3.6 13.6 - - + +
176B ASN* 2.8 26.5 + - - +
36C ALA 5.2 0.4 - - - +
37C ILE* 5.2 6.7 - - + -
38C PRO* 4.1 25.8 - - + -
23D PRO 6.0 0.7 - - - +
26D GLN 5.7 0.4 - - - +
27D LYS* 1.3 80.2 - - - +
29D ASN* 1.3 78.8 + - - +
30D ILE* 4.7 0.2 - - + -
36D ALA* 3.1 26.0 - - + -
37D ILE* 3.4 11.7 - - - +
39D SER* 4.1 0.2 - - - -
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Residues in contact with ASN 29 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176B ASN* 2.7 37.4 + - - +
179B THR* 3.2 16.3 - - - +
180B PRO* 5.3 4.3 - - + -
23C PRO* 5.7 0.6 - - - +
28D VAL* 1.3 79.2 - - - +
30D ILE* 1.3 63.6 + - - +
36D ALA* 3.1 2.3 - - - -
37D ILE* 2.6 46.7 + - + -
38D PRO 3.9 3.4 + - - -
39D SER* 3.0 33.4 + - - +
41D VAL* 5.9 0.2 - - - +
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Residues in contact with ILE 30 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146B THR* 3.9 17.7 - - + +
172B LEU* 4.8 4.5 - - + -
175B VAL* 3.3 42.0 - - + -
179B THR* 3.2 10.9 + - + -
180B PRO* 3.3 18.0 - - - +
181B ASN* 3.2 27.1 - - - +
182B VAL* 4.3 7.9 - - + -
28D VAL* 4.7 1.3 - - + -
29D ASN* 1.3 85.6 - - - +
31D ASP* 1.3 78.2 + - - +
34D GLY* 3.6 18.4 - - - +
35D ASN 3.1 13.9 - - - +
36D ALA* 4.6 1.8 - - + -
37D ILE* 4.1 3.4 - - - -
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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
------------------------------------------------------------
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