Contacts of the strand formed by residues 41 - 45 (chain D) in PDB entry 2XEW
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 41 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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27D LYS* 3.0 70.9 + - - +
30D ILE* 3.3 30.0 - - + +
36D ILE* 2.8 39.7 + - + -
37D PRO 3.6 7.6 - - - +
38D PRO* 2.9 21.4 + - - +
39D ASP 3.2 0.8 - - - -
40D GLN* 1.3 78.2 - - - +
42D ARG* 1.3 60.2 + - - +
43D LEU* 4.5 0.6 - - + +
69D LEU* 3.9 14.7 - - + +
70D VAL 4.0 1.8 - - - -
72D ARG* 3.7 11.2 + - - -
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Residues in contact with ARG 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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27D LYS* 4.7 1.8 - - - +
41D GLN* 1.3 73.0 - - - +
43D LEU* 1.3 62.4 + - - +
44D ILE* 4.1 18.1 - - + +
49D GLN* 2.7 54.4 + - + +
68D HIS 3.6 0.9 - - - +
69D LEU* 3.6 1.4 - - - +
70D VAL* 2.7 53.6 + - + +
71D LEU 4.5 0.4 + - - -
72D ARG* 4.2 20.6 - - + +
75G GLY 3.6 18.4 + - - -
76G GLY* 3.5 6.5 - - - -
11H LYS* 3.0 37.6 - - - +
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Residues in contact with LEU 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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5D VAL* 4.1 7.9 - - + -
23D ILE* 4.1 15.3 - - + -
26D VAL* 3.8 27.1 - - + -
27D LYS* 3.9 30.6 - - + +
30D ILE* 3.6 22.9 - - + -
41D GLN* 4.1 0.8 + - - +
42D ARG* 1.3 75.2 - - - +
44D ILE* 1.3 63.4 + - - +
49D GLN* 3.6 1.2 - - - -
50D LEU* 2.8 45.7 + - + +
67D LEU* 4.4 13.7 - - + -
68D HIS 3.2 11.2 - - - +
69D LEU* 3.9 17.3 - - + -
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Residues in contact with ILE 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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8D LEU* 6.4 0.4 - - + -
42D ARG* 4.1 25.1 - - + +
43D LEU* 1.3 81.4 - - - +
45D PHE* 1.3 67.4 + - - +
47D GLY* 4.0 22.4 - - - +
48D LYS 3.1 13.7 - - - +
49D GLN* 4.4 7.6 - - + +
50D LEU* 4.3 2.2 - - - -
66D THR 4.7 0.2 - - - +
67D LEU* 3.6 3.5 - - - +
68D HIS* 2.8 54.0 + - + +
70D VAL* 4.3 21.1 - - + -
9H THR* 5.6 2.2 - - - +
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Residues in contact with PHE 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 ILE* 1.3 75.6 - - - +
46D ALA* 1.3 84.9 - - + +
47D GLY 3.1 2.2 - - - +
48D LYS* 3.0 24.5 + - - +
50D LEU* 3.8 23.3 - - + +
59D TYR* 3.6 22.4 - + + -
60D ASN* 4.2 5.2 - - + -
61D ILE* 3.4 30.5 - - + -
62D GLN* 6.0 0.2 - - - -
65D SER* 4.0 14.1 - - - -
66D THR 3.5 17.7 - - - -
67D LEU* 3.7 10.8 - - + -
1077D EDO 3.6 41.3 - - - -
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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