Contacts of the strand formed by residues 57 - 64 (chain C) in PDB entry 2IVF
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 ARG 57 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28C THR* 3.1 33.2 + - + +
29C PHE 3.4 4.9 - - - +
30C GLU* 5.5 0.4 - - - -
31C MET* 4.0 3.5 - - - +
55C ILE* 3.5 9.0 - - - +
56C LYS* 1.3 83.3 - - + +
58C LEU* 1.3 59.7 + - - +
59C ASP* 3.1 33.5 + - - +
74C LYS 5.0 0.2 - - - -
75C TRP* 3.5 21.0 - - - +
76C ALA 4.7 1.7 + - - -
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Residues in contact with LEU 58 (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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27C THR 3.7 1.0 - - - +
29C PHE* 2.8 35.6 + - + +
31C MET* 3.8 23.8 - - + +
57C ARG* 1.3 75.1 - - - +
59C ASP* 1.3 63.9 + - - +
60C VAL* 3.8 9.6 - - + -
73C LEU* 4.0 15.9 - - + -
74C LYS 3.6 15.9 - - - +
75C TRP* 3.5 35.0 - - + -
93C VAL* 4.2 11.0 - - + -
187C PHE* 3.4 39.3 - - + -
188C ALA 4.8 0.2 - - - +
189C VAL* 4.9 4.7 - - + -
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Residues in contact with ASP 59 (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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26C SER* 4.2 13.6 + - - +
27C THR 3.6 3.4 - - - -
28C THR* 3.0 36.3 + - - +
57C ARG* 3.1 27.1 + - - -
58C LEU* 1.3 71.5 - - - +
60C VAL* 1.3 62.6 + - - +
72C ARG 3.6 0.9 - - - +
73C LEU* 3.3 4.3 - - - -
74C LYS* 2.9 59.1 + - + +
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Residues in contact with VAL 60 (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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1C MET* 3.8 20.0 - - + +
25C GLU 3.8 0.2 - - - +
26C SER* 3.5 3.8 + - - -
27C THR 2.9 30.6 + - - +
29C PHE* 4.0 14.4 - - + -
58C LEU* 3.8 19.3 - - + -
59C ASP* 1.3 80.3 - - - +
61C ALA* 1.3 69.2 + - - +
71C LEU* 4.1 9.2 - - + -
72C ARG 3.2 9.0 - - - +
73C LEU* 4.0 12.1 - - + -
187C PHE* 3.8 40.8 - - + -
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Residues in contact with ALA 61 (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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1C MET* 4.3 0.2 - - - -
21C TRP* 3.7 16.4 - - + +
24C ALA* 3.6 27.4 - - + -
25C GLU 3.6 9.2 - - - +
26C SER* 4.4 10.8 - - - +
60C VAL* 1.3 77.0 - - - +
62C ALA* 1.3 62.6 + - - +
71C LEU* 3.4 3.1 - - - -
72C ARG* 2.8 38.7 + - + +
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Residues in contact with ALA 62 (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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1C MET* 3.8 9.6 - - + +
2C LYS 3.8 4.6 + - - +
3C ALA* 3.5 16.0 - - + -
4C LYS* 3.4 17.0 + - - +
24C ALA* 4.9 1.7 - - - +
25C GLU* 4.1 6.0 + - - +
61C ALA* 1.3 77.3 - - - +
63C LEU* 1.3 68.7 + - - +
69C ILE* 5.6 0.2 - - + -
70C ALA 3.4 5.4 - - - +
71C LEU* 3.7 22.0 - - + -
210C PHE* 3.7 21.1 - - + -
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Residues in contact with LEU 63 (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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3C ALA* 4.8 0.4 - - - -
4C LYS* 3.3 23.6 - - + +
6C VAL* 3.4 22.7 - - + -
13C LEU* 3.7 15.9 - - + -
20C ILE* 3.8 35.4 - - + +
21C TRP* 3.7 35.8 - - + -
23C GLY 5.8 0.4 - - - -
24C ALA* 4.0 18.4 - - + -
25C GLU 5.4 0.2 - - - +
62C ALA* 1.3 81.2 - - - +
64C HIS* 1.3 59.1 + - - +
69C ILE* 3.6 3.2 - - - +
70C ALA* 2.7 40.1 + - - +
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Residues in contact with HIS 64 (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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3C ALA* 3.4 25.8 + - + -
4C LYS 2.9 10.3 + - - -
5C ARG* 3.3 25.1 + - + -
6C VAL* 2.7 35.2 + - - +
13C LEU* 4.1 6.7 - - - -
63C LEU* 1.3 74.6 - - - +
65C ASN* 1.3 55.3 + - - +
66C GLY 3.1 19.0 + - - -
68C MET 3.3 15.0 - - - +
69C ILE* 3.8 8.1 - - + -
168C MET* 3.6 15.7 - - + -
179C ALA* 4.0 7.9 - - + -
212C ILE* 3.6 13.8 - - + +
213C LEU 2.7 29.6 + - - -
214C LYS* 3.9 15.5 - - + -
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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