Contacts of the strand formed by residues 32 - 40 (chain D) in PDB entry 3ZWG
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 LYS 32 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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23D LEU* 2.8 44.1 + - + +
24D GLU* 3.9 8.7 - - - +
26D LEU* 3.7 22.7 - - + -
27D GLY 2.8 22.1 + - - +
28D ASN* 4.9 0.6 + - - +
29D VAL* 3.6 22.2 - - + -
31D ARG* 1.3 77.6 - - - +
33D ILE* 1.3 62.0 + - - +
75D GLY 3.5 6.1 - - - +
76D GLN* 4.2 0.7 - - + +
86D VAL* 4.5 5.9 - - - +
106D VAL* 4.9 0.5 - - - +
168D GLY 3.2 8.4 + - - +
169D HIS* 3.4 41.5 + - + -
170D ALA* 2.8 25.8 + - - +
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Residues in contact with ILE 33 (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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23D LEU* 3.8 4.3 - - - -
26D LEU* 4.4 0.7 - - - +
32D LYS* 1.3 76.0 - - - +
34D ALA* 1.3 70.6 + - - +
35D VAL* 3.9 15.3 - - + -
74D ASN* 3.2 8.9 - - - +
75D GLY* 2.9 42.9 + - - +
86D VAL* 4.4 4.3 - - + -
104D PHE* 3.8 50.3 - - + -
106D VAL* 4.0 8.3 - - + -
164D MET* 3.9 21.1 - - + -
170D ALA* 3.3 18.4 - - + +
172D LEU* 4.2 7.9 - - + +
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Residues in contact with ALA 34 (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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19D LEU* 3.6 28.8 - - + +
22D VAL* 3.5 26.9 - - + -
23D LEU* 3.6 13.1 - - + +
33D ILE* 1.3 74.6 - - - +
35D VAL* 1.3 61.4 + - - +
73D TYR 3.7 4.5 - - - -
170D ALA 2.9 11.4 + - - +
171D ILE* 3.7 3.5 - - + -
172D LEU 3.0 26.0 + - - +
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Residues in contact with VAL 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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19D LEU* 3.8 7.6 - - - +
33D ILE* 3.9 31.2 - - + +
34D ALA* 1.3 78.3 - - - +
36D GLY* 1.3 63.0 + - - +
37D ILE* 4.1 23.8 - - + -
71D LEU* 5.6 0.2 - - + -
72D LEU* 3.6 3.3 - - - +
73D TYR* 2.9 51.2 + - + +
90D ILE* 4.5 12.3 - - + -
102D VAL* 5.3 1.1 - - + -
104D PHE* 4.8 11.0 - - + -
172D LEU* 3.5 24.7 - - + +
174D ILE* 5.3 0.7 - - + -
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Residues in contact with GLY 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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14D LEU* 3.7 13.3 - - - +
19D LEU* 3.7 13.3 - - - +
35D VAL* 1.3 77.1 - - - +
37D ILE* 1.3 66.5 + - - +
71D LEU* 3.2 11.7 - - - -
72D LEU* 4.5 0.2 - - - -
172D LEU 3.0 11.9 + - - +
173D GLU* 3.7 1.7 - - - -
174D ILE* 3.0 25.6 + - - +
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Residues in contact with ILE 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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14D LEU* 3.7 4.7 - - - +
35D VAL* 4.1 19.1 - - + -
36D GLY* 1.3 79.2 - - - +
38D ASP* 1.3 63.2 + - - +
39D ASN* 3.7 0.9 + - - +
45D TRP* 3.5 30.8 - - + -
65D VAL* 5.1 0.2 - - - +
70D ALA* 3.1 2.4 - - - -
71D LEU* 2.9 55.5 + - + +
90D ILE* 4.9 11.0 - - + -
92D TYR* 5.4 2.0 - - + -
100D LEU* 4.8 3.1 - - + -
102D VAL* 4.0 29.6 - - + -
174D ILE* 3.3 23.6 - - + +
176D VAL* 4.6 3.1 - - + -
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Residues in contact with ASP 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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11D GLY* 3.2 31.3 - - - +
14D LEU* 3.7 6.1 - - + +
37D ILE* 1.3 72.4 - - - +
39D ASN* 1.3 67.1 + - - +
40D GLU* 2.7 38.1 + - - +
45D TRP* 3.8 6.0 - - - -
69D LYS 3.9 0.3 - - - +
70D ALA* 3.9 6.3 - - - -
174D ILE 2.9 6.7 + - - -
175D HIS* 3.1 39.6 + - + +
176D VAL 3.1 22.2 + - - +
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Residues in contact with ASN 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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37D ILE 3.7 0.4 + - - -
38D ASP* 1.3 73.1 + - - +
40D GLU* 1.3 55.3 + - - +
41D SER* 2.5 27.5 + - - -
43D LYS 3.1 18.4 + - - +
45D TRP* 3.0 27.8 - - + +
65D VAL* 3.0 36.5 + - + -
66D ALA 3.3 10.1 + - - -
67D HIS* 3.6 1.5 - - - -
68D GLY* 2.6 36.4 + - - -
69D LYS 2.8 21.9 + - - +
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Residues in contact with GLU 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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11D GLY* 4.1 4.2 - - - -
38D ASP* 2.7 36.7 - - - +
39D ASN* 1.3 73.4 - - - +
41D SER* 1.3 61.8 + - - +
42D GLY 3.2 5.0 + - - -
67D HIS* 3.4 28.6 + - + -
68D GLY* 3.3 20.3 - - - +
176D VAL 2.8 17.4 + - - +
177D THR* 3.8 20.4 - - + -
178D LYS* 3.4 17.3 + - - -
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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
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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