Contacts of the strand formed by residues 24 - 29 (chain D) in PDB entry 2Z3Q
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 ARG 24 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57A ALA* 5.4 0.8 - - - +
20C HIS 4.5 17.6 + - - -
21C ILE* 4.8 9.3 - - - +
22C ASP* 5.3 5.7 + - - -
53C GLU* 3.3 34.2 + - - +
54C SER 5.7 0.4 + - - -
22D TYR 3.4 9.6 + - - +
23D SER* 1.3 76.4 + - - +
25D GLU* 1.4 73.4 + - - +
42D LEU* 3.7 27.7 - - + +
43D THR 3.6 4.3 - - - -
44D GLU* 3.4 36.2 + - + +
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Residues in contact with GLU 25 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14D ILE* 4.1 17.7 - - + -
15D TRP 3.7 5.7 - - - +
16D VAL* 3.5 10.6 - - + -
17D LYS* 3.0 39.1 + - - +
18D SER* 3.2 16.1 + - - -
23D SER* 3.0 17.1 + - - +
24D ARG* 1.4 79.9 - - - +
26D ARG* 1.3 68.4 + - - +
42D LEU* 3.5 4.6 - - - +
43D THR* 2.8 37.2 + - + -
56D TRP* 3.6 25.8 - - + -
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Residues in contact with ARG 26 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22C ASP* 2.9 33.7 + - - -
23C ALA* 3.4 17.1 - - - +
53C GLU* 2.7 45.2 + - - -
14D ILE* 3.6 16.6 - - - +
15D TRP* 4.8 2.8 + - - +
24D ARG* 5.4 0.6 - - - +
25D GLU* 1.3 82.7 + - - +
27D TYR* 1.3 64.2 + - - +
28D ILE* 3.8 14.8 - - + +
41D SER* 3.1 32.8 + - - +
42D LEU* 3.8 15.7 - - + +
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Residues in contact with TYR 27 (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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6D PRO* 3.4 13.8 - - + +
7D MET* 2.6 33.5 + - - +
8D SER* 4.6 1.3 - - - -
9D VAL* 3.6 30.1 - - + +
12D ALA* 4.3 4.0 - - + -
13D ASP* 3.3 13.0 - - - +
14D ILE* 3.8 31.9 - - + -
26D ARG* 1.3 75.4 - - - +
28D ILE* 1.3 62.0 + - - +
29D CYS 4.3 0.5 + - - -
41D SER* 3.0 35.9 + - - +
43D THR* 3.7 24.2 + - + -
56D TRP* 5.4 1.2 - - - +
57D THR 5.3 0.5 + - - -
59D PRO* 3.7 28.4 - - + +
61D LEU* 3.4 21.4 - - + +
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Residues in contact with ILE 28 (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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12D ALA* 4.2 2.0 - - - -
13D ASP* 2.7 33.2 + - - +
15D TRP* 3.9 31.6 - - + -
26D ARG* 3.8 16.6 - - + +
27D TYR* 1.3 79.0 - - - +
29D CYS* 1.3 75.4 + - - +
30D ASN* 4.2 0.7 - - - +
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Residues in contact with CYS 29 (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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11D HIS 3.5 5.2 - - - +
27D TYR 4.2 1.0 + - - -
28D ILE* 1.3 83.9 - - - +
30D ASN* 1.3 66.4 + - - +
31D SER 3.7 0.7 + - - -
33D PHE* 3.7 21.7 - - + +
34D LYS* 3.6 1.1 - - - -
35D ARG* 3.5 30.1 - - - +
61D LEU* 4.0 7.0 - - - -
63D CYS* 2.1 49.8 - - + -
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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