Contacts of the strand formed by residues 48 - 53 (chain C) in PDB entry 2W3S
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 THR 48 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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35C THR* 5.0 1.7 + - - +
45C GLY* 2.5 29.0 + - - -
46C ALA 3.4 2.0 + - - -
47C CYS* 1.3 76.8 - - - +
49C VAL* 1.3 65.3 + - - +
59C ALA* 3.9 13.9 - - + -
60C VAL 3.2 13.5 - - - +
61C ASN* 3.9 2.2 + - - -
78C ILE 5.5 0.2 + - - -
108C PRO 5.2 0.3 - - - -
109C GLY* 3.6 15.0 - - - +
112C VAL* 3.4 34.4 - - + +
113C SER* 3.7 20.0 - - - +
132C ASN* 3.4 8.0 + - - -
274C GLN* 3.5 12.3 + - + +
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Residues in contact with VAL 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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23C LEU* 4.1 13.9 - - + -
27C LEU* 4.1 7.2 - - + -
35C THR* 4.2 7.4 - - - +
47C CYS 3.1 7.2 + - - +
48C THR* 1.3 78.2 - - - +
50C MET* 1.3 58.4 + - - +
51C ILE* 4.7 0.2 - - + -
59C ALA* 3.3 1.0 - - - -
60C VAL* 2.5 65.7 + - + +
62C ALA* 3.7 26.5 - - + +
75C LEU* 3.9 9.4 - - + -
76C ARG 3.9 5.6 - - - +
77C THR* 3.7 28.9 - - + -
112C VAL* 3.5 6.3 - - - -
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Residues in contact with MET 50 (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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49C VAL* 1.3 73.6 - - - +
51C ILE* 1.3 67.9 + - - +
52C ARG* 4.4 4.3 - - - +
57C SER* 3.0 33.9 - - - +
58C ARG 3.4 11.2 - - - +
59C ALA* 4.1 0.7 - - - +
74C ALA 3.8 0.5 - - - +
75C LEU* 3.9 0.3 - - - +
76C ARG* 2.8 58.8 + - + +
81C ILE* 5.1 7.4 - - + -
112C VAL* 3.4 15.2 - - + +
115C ALA* 4.4 3.4 - - - +
116C ALA* 3.5 37.5 - - + -
119C ASP* 3.7 16.6 - - + -
158C LEU* 5.3 9.0 - - + -
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Residues in contact with ILE 51 (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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23C LEU* 5.2 0.2 - - + -
49C VAL* 4.7 2.2 - - + -
50C MET* 1.3 78.9 - - - +
52C ARG* 1.3 61.4 + - - +
56C GLY 4.1 0.2 - - - +
57C SER* 3.3 5.0 - - - -
58C ARG* 2.8 75.7 + - + +
60C VAL* 4.1 23.8 - - + -
65C MET* 4.8 15.7 - - + -
70C ILE* 4.7 15.3 - - + -
73C LYS* 3.9 24.5 - - + -
74C ALA 3.5 5.8 - - - +
75C LEU* 3.8 21.1 - - + -
278C VAL* 5.6 1.8 - - + -
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Residues in contact with ARG 52 (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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50C MET* 4.4 5.0 - - + +
51C ILE* 1.3 77.6 - - - +
53C ASP* 1.3 72.7 + - - +
56C GLY* 3.3 19.4 - - - +
57C SER* 3.8 16.4 - - - +
58C ARG* 5.2 0.7 - - - +
73C LYS* 3.3 9.0 - - - +
74C ALA* 2.8 44.8 + - + +
119C ASP* 3.1 40.5 + - - -
158C LEU* 3.2 28.6 + - - +
159C GLN* 3.9 10.7 + - - +
161C ASP* 3.9 11.8 - - - +
162C ALA* 3.7 31.8 - - - +
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Residues in contact with ASP 53 (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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52C ARG* 1.3 82.8 - - - +
54C ALA* 1.3 65.0 + - - +
55C ALA* 2.9 13.2 + - - +
56C GLY* 3.0 14.9 + - - +
58C ARG* 2.5 43.0 + - - -
72C GLY 5.4 2.2 - - - +
73C LYS* 3.2 35.3 + - + +
162C ALA* 5.9 1.0 - - - -
165C THR* 6.4 1.8 - - - -
166C LEU* 6.0 1.8 - - - -
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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