Contacts of the strand formed by residues 34 - 45 (chain D) in PDB entry 2WJ7
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 VAL 34 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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30D VAL* 3.5 5.4 - - - -
31D LEU* 3.1 37.2 + - + +
32D GLY 3.2 3.0 - - - -
33D ASP* 1.3 85.3 - - + +
35D ILE* 1.3 66.3 + - - +
36D GLU* 3.7 8.5 + - + +
58D LYS* 3.7 35.7 - - + -
59D TYR 3.3 15.0 - - - +
60D ARG* 5.4 7.0 - - + -
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Residues in contact with ILE 35 (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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14D VAL* 6.1 4.7 - - + -
28D VAL* 4.4 13.2 - - + -
29D LYS 3.8 4.0 - - - +
30D VAL* 4.4 15.9 - - + +
33D ASP 4.1 0.8 + - - -
34D VAL* 1.3 71.2 - - - +
36D GLU* 1.3 68.0 + - - +
37D VAL* 4.2 9.6 - - + -
57D ARG 3.6 0.5 - - - +
58D LYS* 3.1 5.5 - - - -
59D TYR* 3.0 62.1 + - + +
60D ARG 5.4 0.7 - - - +
61D ILE* 5.2 12.8 - - + -
62D PRO* 6.3 0.7 - - + -
70D ILE* 4.3 17.9 - - + -
82D VAL* 4.0 28.9 - - + -
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Residues in contact with GLU 36 (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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27D LYS* 3.7 2.1 - - + +
28D VAL* 3.4 6.8 - - - +
29D LYS* 2.9 40.2 + - + +
31D LEU* 2.9 38.2 - - + +
34D VAL* 4.4 10.8 - - + +
35D ILE* 1.3 75.5 - - - +
37D VAL* 1.3 62.5 + - - +
38D HIS* 6.2 0.2 - - + -
56D HIS* 3.5 22.2 + - + -
57D ARG 3.2 4.5 - - - -
58D LYS* 3.8 26.7 + - + +
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Residues in contact with VAL 37 (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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16D LEU* 4.3 10.8 - - + -
26D LEU* 5.0 2.7 - - + -
27D LYS 3.4 7.9 - - - +
28D VAL* 4.4 10.8 - - + -
35D ILE* 4.2 15.5 - - + -
36D GLU* 1.3 77.1 - - - +
38D HIS* 1.3 66.7 + - - +
55D PHE* 3.8 27.3 - - + -
56D HIS* 3.2 4.7 + - - -
57D ARG* 2.9 36.0 + - + -
59D TYR* 4.3 16.8 - - + -
80D LEU* 3.9 24.9 - - + -
82D VAL* 5.0 5.8 - - + -
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Residues in contact with HIS 38 (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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25D GLU 3.7 2.3 - - - +
26D LEU* 3.4 7.3 - - - +
27D LYS* 2.9 50.1 + - + -
36D GLU* 4.2 0.4 - - + -
37D VAL* 1.3 78.7 - - - +
39D GLY* 1.3 60.4 + - - +
40D LYS* 3.8 15.1 - - + +
54D GLU* 2.7 41.5 + - + -
55D PHE* 3.2 15.1 + - - -
56D HIS* 4.0 25.0 - + + +
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Residues in contact with GLY 39 (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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21D PHE* 3.8 7.4 - - - -
25D GLU 3.5 7.0 - - - -
26D LEU* 3.8 6.7 - - - -
38D HIS* 1.3 75.1 - - - +
40D LYS* 1.3 66.0 + - - +
54D GLU* 3.2 2.1 - - - +
55D PHE* 2.8 55.2 + - - +
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Residues in contact with LYS 40 (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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21D PHE* 3.3 5.7 - - - -
25D GLU* 2.9 37.3 + - - +
38D HIS* 3.8 13.0 - - + +
39D GLY* 1.3 75.7 - - - +
41D HIS* 1.3 76.9 + - - +
42D GLU* 5.2 5.4 - - - +
53D ARG 3.3 8.1 - - - +
54D GLU* 3.4 42.3 + - + +
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Residues in contact with HIS 41 (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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20D HIS 3.5 13.3 + - - -
21D PHE* 3.7 13.2 - - + -
25D GLU* 3.4 26.5 - - - +
40D LYS* 1.3 86.1 - - - +
42D GLU* 1.3 85.0 + - - +
44D ARG* 3.5 22.9 - - - -
51D ILE* 3.0 22.4 + - - +
52D SER* 3.2 8.6 - - - -
53D ARG* 2.6 65.8 + - + +
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Residues in contact with GLU 42 (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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25D GLU* 4.8 1.8 + - - -
40D LYS* 5.2 7.2 - - - +
41D HIS* 1.3 93.8 - - - +
43D GLU* 1.3 71.6 + - - +
44D ARG* 3.8 2.9 + - - +
52D SER* 3.7 2.9 - - - -
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Residues in contact with GLU 43 (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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56C HIS* 5.6 3.4 - - - +
58C LYS* 4.0 16.8 - - - +
42D GLU* 1.3 79.0 - - - +
44D ARG* 1.3 63.9 + - - +
50D PHE* 3.4 32.9 - - + +
51D ILE 3.6 11.9 - - - -
52D SER* 3.5 14.0 - - - +
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Residues in contact with ARG 44 (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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20D HIS* 2.8 28.1 + - - +
22D SER* 4.8 3.2 + - - +
25D GLU* 3.3 35.6 + - - -
41D HIS* 3.5 23.9 - - - -
42D GLU 3.8 5.6 + - - +
43D GLU* 1.3 81.1 - - - +
45D GLN* 1.3 75.9 + - - +
46D ASP* 5.5 0.9 - - - -
50D PHE* 4.2 2.2 - - - -
51D ILE* 3.1 41.9 + - - +
53D ARG* 4.5 2.6 - - - +
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Residues in contact with GLN 45 (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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44D ARG* 1.3 89.9 - - - +
46D ASP* 1.3 77.2 + - - +
49D GLY* 3.1 17.7 - - - +
50D PHE* 4.2 13.2 - - + +
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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