Contacts of the strand formed by residues 43 - 49 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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39C LEU* 3.2 25.5 + - + +
40C THR 3.4 15.7 - - - +
41C GLY 3.1 0.6 - - - -
42C SER* 1.3 73.4 - - - +
44C GLY* 1.3 62.1 + - - +
55C HIS* 2.7 38.0 + - - -
57C ASN* 3.8 17.7 + - - +
58C GLU* 4.3 4.2 + - - +
126C MSE 4.5 0.3 - - - +
128C ALA* 3.5 31.5 + - + +
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Residues in contact with GLY 44 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38C THR* 2.8 26.6 + - - -
42C SER 3.3 1.0 + - - -
43C ASP* 1.3 77.8 + - - +
45C GLU* 1.3 72.3 + - - +
46C VAL 4.3 0.2 - - - -
55C HIS* 3.7 3.4 - - - -
56C ALA 3.4 12.1 - - - -
57C ASN* 4.1 4.9 - - - -
126C MSE 2.7 31.0 + - - +
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Residues in contact with GLU 45 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37C ALA 3.9 1.7 - - - +
38C THR* 5.5 0.7 - - - -
44C GLY* 1.3 78.8 - - - +
46C VAL* 1.3 62.8 + - - +
47C ILE* 3.5 6.2 - - + +
55C HIS* 3.3 5.5 - - - -
56C ALA* 2.8 35.1 + - + +
124C ARG* 2.9 32.6 + - - +
125C MSE 3.8 8.1 - - - -
126C MSE 2.8 26.8 + - - +
175C HIS* 3.2 28.2 + - + +
185C GLY* 3.7 18.8 - - - -
186C HIS* 3.5 17.5 - - - +
803C ZN 3.8 3.6 - - - -
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Residues in contact with VAL 46 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25C ILE* 4.2 2.5 - - + -
36C ILE* 3.5 1.4 - - - -
37C ALA* 2.8 31.8 + - + +
38C THR* 3.8 16.6 - - - +
39C LEU* 3.7 33.0 - - + -
45C GLU* 1.3 74.8 - - - +
47C ILE* 1.3 65.7 + - - +
48C PHE* 4.0 32.5 - - + -
53C ALA* 4.8 0.7 - - + -
54C TYR 3.2 8.5 - - - +
55C HIS* 4.0 6.1 - - + -
65C LEU* 4.2 14.8 - - + -
175C HIS* 2.8 19.4 + - - -
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Residues in contact with ILE 47 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35C GLY 3.9 2.0 - - - -
45C GLU* 3.5 24.2 - - + +
46C VAL* 1.3 77.9 - - - +
48C PHE* 1.3 67.0 + - - +
49C LEU* 3.5 11.1 + - + -
52C LYS 3.4 2.3 - - - +
53C ALA* 3.7 0.2 - - - -
54C TYR* 2.8 47.8 + - + +
56C ALA* 4.6 1.8 - - + +
62C PHE* 4.3 20.2 - - + -
154C ALA 5.6 0.2 - - - +
156C VAL* 3.6 26.7 - - + -
175C HIS* 3.8 15.7 - - + +
176C PHE 3.8 22.9 - - - +
177C ALA* 4.3 14.1 - - + +
185C GLY 4.6 4.0 - - - +
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Residues in contact with PHE 48 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25C ILE* 4.1 17.0 - - + -
28C LEU* 4.0 20.4 - - + -
29C LEU* 3.7 27.8 - - + -
33C ASN 3.9 4.7 - - - -
34C LEU* 3.2 12.1 - - - +
35C GLY* 2.9 53.4 + - - +
36C ILE* 3.7 5.4 - - - -
37C ALA* 3.9 23.1 - - + -
46C VAL* 4.0 12.3 - - + -
47C ILE* 1.3 72.8 - - - +
49C LEU* 1.3 59.3 + - - +
52C LYS 3.3 2.5 - - - +
53C ALA* 3.8 24.9 - - + -
74C ALA* 4.4 7.0 - - + -
75C SER 4.2 2.0 - - - -
76C ILE* 3.6 19.7 - - + -
156C VAL* 3.9 8.1 - - - +
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Residues in contact with LEU 49 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33C ASN 3.8 1.0 + - - -
34C LEU* 4.9 2.5 - - + +
47C ILE* 3.5 10.5 + - + -
48C PHE* 1.3 75.2 - - - +
50C ASP* 1.3 88.3 + - - +
51C GLY 3.2 1.3 - - - -
52C LYS* 2.9 27.3 + - - +
54C TYR* 4.1 11.3 + - + -
113C LYS* 4.1 13.9 - - - +
154C ALA* 4.0 27.8 - - + +
156C VAL* 3.7 24.2 - - + -
177C ALA* 4.0 21.3 - - + +
181C ARG* 3.4 30.4 + - - +
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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