Contacts of the strand formed by residues 34 - 38 (chain C) in PDB entry 2VM8
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 34 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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18C LEU* 4.6 5.5 - - + +
19C ILE 3.2 11.2 - - - +
20C LYS* 3.9 21.9 - - - +
21C GLY* 3.0 22.9 + - - -
33C ALA* 1.3 75.9 - - - +
35C ILE* 1.3 63.6 + - - +
45C ILE* 3.4 8.0 - - - +
46C GLY 2.9 35.0 + - - +
47C GLU* 4.4 4.1 - - - +
48C ASN* 4.0 17.8 + - - -
49C LEU* 3.7 15.1 + - + +
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Residues in contact with ILE 35 (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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18C LEU* 3.5 4.5 - - - -
19C ILE* 2.9 43.8 + - + +
24C ILE* 4.0 21.8 - - + -
33C ALA 4.2 3.1 - - - +
34C ASP* 1.3 78.7 - - - +
36C TYR* 1.3 61.2 + - - +
37C MET* 3.7 12.8 - - + +
42C ILE* 3.7 26.9 - - + -
44C GLN 3.7 2.9 - - - +
45C ILE* 4.5 1.3 - - + -
65C VAL* 3.5 36.8 - - + -
401C ILE* 3.9 18.6 - - + -
409C LEU* 3.6 21.5 - - + -
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Residues in contact with TYR 36 (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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16C ARG* 3.1 18.0 + - - +
17C LEU 3.2 14.8 - - - -
18C LEU* 3.9 7.6 - - + -
35C ILE* 1.3 73.6 - - - +
37C MET* 1.3 69.1 + - - +
38C GLU* 2.5 35.3 + - + -
42C ILE* 3.6 1.9 - - - +
43C LYS* 2.7 47.3 + - + -
44C GLN* 3.0 34.9 + - + +
49C LEU* 4.1 2.6 - - + +
51C VAL* 3.3 30.5 - - + -
52C PRO* 3.6 13.3 - - + +
55C VAL* 3.7 24.9 - - + -
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Residues in contact with MET 37 (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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15C ASP 4.2 2.5 - - - -
17C LEU* 3.0 62.2 + - + +
19C ILE* 3.7 27.1 - - + -
35C ILE* 3.7 22.9 - - + +
36C TYR* 1.3 85.9 - - - +
38C GLU* 1.3 67.4 + - - +
41C LEU 3.1 10.5 - - - +
42C ILE* 4.0 15.7 - - + -
43C LYS* 4.2 0.4 - - - +
407C ALA* 3.9 29.6 - - + -
409C LEU* 4.0 18.6 - - + -
447C ILE* 4.4 8.5 - - + -
450C GLY* 4.8 3.6 - - - -
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Residues in contact with GLU 38 (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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15C ASP 3.7 7.5 + - - -
16C ARG* 3.4 22.9 + - + -
36C TYR* 2.5 32.9 + - + +
37C MET* 1.3 77.7 - - - +
39C ASP* 1.3 87.3 + - - +
40C GLY 3.4 1.3 + - - +
41C LEU 2.9 11.8 + - - +
43C LYS* 3.2 47.6 + - + +
52C PRO* 4.6 1.0 - - - +
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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