Contacts of the strand formed by residues 43 - 49 (chain D) in PDB entry 1XV2
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 ASP 43 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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39D LEU* 3.1 24.9 + - + +
40D THR 3.3 15.3 - - - +
41D GLY 3.1 0.6 - - - -
42D SER* 1.3 73.0 - - - +
44D GLY* 1.3 59.8 + - - +
55D HIS* 2.7 37.4 + - - -
57D ASN* 3.8 18.9 + - - +
58D GLU* 4.5 3.1 - - - +
126D MSE 4.5 0.2 - - - +
128D ALA* 3.5 32.1 + - + +
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Residues in contact with GLY 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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38D THR* 2.8 25.4 + - - -
42D SER 3.2 1.8 + - - -
43D ASP* 1.3 77.2 + - - +
45D GLU* 1.3 72.8 + - - +
46D VAL 4.3 0.2 - - - -
55D HIS* 3.7 2.9 - - - -
56D ALA 3.4 11.7 - - - -
57D ASN* 4.3 4.0 - - - -
126D MSE 2.8 31.6 + - - +
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Residues in contact with GLU 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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37D ALA 4.0 1.1 - - - +
38D THR* 5.7 0.3 - - - -
44D GLY* 1.3 80.9 - - - +
46D VAL* 1.3 63.2 - - - +
47D ILE* 3.6 4.1 - - + +
55D HIS* 3.2 5.4 - - - -
56D ALA* 2.8 40.1 + - + +
124D ARG* 2.9 25.0 + - - +
125D MSE 3.8 7.6 - - + -
126D MSE 2.8 28.8 + - - +
175D HIS* 3.2 29.5 + - + +
185D GLY* 3.6 22.0 - - - -
186D HIS* 3.3 24.6 - - - +
804D ZN 3.7 3.8 - - - -
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Residues in contact with VAL 46 (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 ILE* 4.3 2.5 - - + -
36D ILE* 3.5 1.6 - - - -
37D ALA* 3.0 31.6 + - + -
38D THR* 3.9 14.1 - - - +
39D LEU* 3.6 34.1 - - + -
45D GLU* 1.3 77.6 - - - +
47D ILE* 1.3 65.6 + - - +
48D PHE* 3.9 35.0 - - + -
53D ALA* 4.8 0.7 - - + -
54D TYR 3.1 8.5 - - - +
55D HIS* 4.2 3.1 - - + -
65D LEU* 4.1 15.7 - - + -
175D HIS* 2.9 19.4 + - - -
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Residues in contact with ILE 47 (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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35D GLY 3.8 1.6 - - - -
45D GLU* 3.6 19.3 - - + +
46D VAL* 1.3 78.9 - - - +
48D PHE* 1.3 65.8 + - - +
49D LEU* 4.4 6.7 - - + -
52D LYS 3.6 2.1 - - - +
54D TYR* 2.8 50.7 + - + +
56D ALA 4.6 2.5 - - - +
62D PHE* 4.2 20.9 - - + -
154D ALA 5.5 0.4 - - - +
156D VAL* 3.7 26.2 - - + -
175D HIS* 3.9 16.8 - - + +
176D PHE* 3.7 23.6 - - - +
177D ALA* 4.2 16.6 - - + +
185D GLY 4.4 8.7 - - - +
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Residues in contact with PHE 48 (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 ILE* 4.0 21.1 - - + -
28D LEU* 4.1 17.9 - - + -
29D LEU* 3.8 21.8 - - + -
33D ASN 3.8 6.1 - - - +
34D LEU* 3.4 9.7 - - - +
35D GLY* 2.9 54.2 + - - +
36D ILE* 4.0 4.7 - - - -
37D ALA* 4.0 22.7 - - + -
46D VAL* 3.9 12.8 - - + -
47D ILE* 1.3 70.5 - - - +
49D LEU* 1.3 60.3 + - - +
52D LYS 3.2 4.0 - - - +
53D ALA* 3.7 29.4 - - + -
71D VAL* 5.5 0.4 - - + -
74D ALA* 4.5 5.6 - - + -
75D SER 4.2 2.0 - - - -
76D ILE* 3.6 23.3 - - + -
156D VAL* 3.9 8.3 - - - +
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Residues in contact with LEU 49 (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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33D ASN 3.8 0.8 + - - -
34D LEU* 5.0 2.0 - - + +
47D ILE* 3.6 10.2 + - + -
48D PHE* 1.3 75.5 - - - +
50D ASP* 1.3 93.9 + - - +
51D GLY 3.1 1.3 - - - -
52D LYS* 2.9 27.9 + - - +
54D TYR* 4.2 11.3 + - + -
113D LYS* 4.0 13.9 - - - -
154D ALA* 4.1 17.0 - - + +
156D VAL* 3.9 23.1 - - + -
177D ALA* 4.0 17.5 - - + -
181D ARG* 3.4 38.3 + - - +
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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