Contacts of the strand formed by residues 34 - 40 (chain C) in PDB entry 2ZVW
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 GLY 34 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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29C ASP 3.2 7.3 - - - +
31C SER* 3.2 24.4 + - - -
33C THR* 1.3 85.5 - - - +
35C PHE* 1.3 62.0 + - - -
36C SER* 3.6 2.9 + - - -
51C LEU* 4.6 4.9 - - - -
52C LEU 3.6 9.4 - - - -
53C ARG* 4.5 1.1 - - - -
54C SER 3.9 2.2 - - - -
60C TYR* 3.0 20.9 - - - -
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Residues in contact with PHE 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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4C LEU* 3.5 26.5 - - + -
12C LEU* 4.4 11.7 - - + -
15C VAL* 6.5 0.2 - - + -
28C PHE* 3.3 50.0 - + + -
29C ASP 3.6 1.8 - - - -
30C CYS* 3.6 24.7 - - - -
34C GLY* 1.3 70.2 - - - -
36C SER* 1.3 59.4 + - - +
50C LEU* 4.6 3.3 - - + +
51C LEU* 3.6 1.1 - - - -
52C LEU* 2.7 65.5 + - + +
57C PHE* 3.8 15.9 - + + -
60C TYR* 3.4 3.1 + - - -
68C MET* 4.1 10.8 - - + -
75C MET* 4.8 3.8 - - + -
90C ILE* 3.8 21.3 - - + -
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Residues in contact with SER 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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28C PHE* 3.4 7.4 - - - -
29C ASP* 2.8 52.9 + - - +
34C GLY 4.6 2.7 + - - -
35C PHE* 1.3 76.1 - - - +
37C LEU* 1.3 64.4 + - - +
50C LEU* 3.1 18.4 - - - -
51C LEU* 4.0 13.2 - - - -
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Residues in contact with LEU 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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19C VAL* 5.0 8.7 - - + -
23C VAL* 6.0 0.7 - - + -
26C ALA* 4.0 16.6 - - + -
27C ASN 3.5 19.7 - - - +
28C PHE* 3.5 34.3 - - + -
29C ASP* 4.7 4.0 - - - -
36C SER* 1.3 80.7 + - - +
38C GLN* 1.3 75.2 + - - +
39C ALA* 4.0 9.4 - - + +
48C VAL* 4.0 20.0 - - + +
49C SER* 3.4 4.0 + - - -
50C LEU* 2.8 52.7 + - + +
72C LEU* 4.5 9.0 - - + -
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Residues in contact with GLN 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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26C ALA* 5.1 1.0 - - - +
27C ASN 4.5 3.4 + - - +
37C LEU* 1.3 79.0 - - - +
39C ALA* 1.3 66.4 + - - +
47C LEU* 4.0 21.9 - - + +
48C VAL 3.2 9.4 - - - +
49C SER* 4.5 10.9 + - - +
123C SER* 4.5 3.6 + - - -
124C GLU 4.4 1.9 - - - +
125C HIS* 2.9 51.5 + - + +
126C LEU* 2.7 49.5 + - - +
128C ILE* 4.3 10.7 - - - +
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Residues in contact with ALA 39 (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 VAL* 4.2 15.5 - - + -
25C ASP 4.9 1.3 - - - +
26C ALA* 3.9 26.0 - - + -
37C LEU* 4.0 5.8 - - + +
38C GLN* 1.3 80.4 - - - +
40C MET* 1.3 65.0 + - - +
47C LEU* 3.4 2.4 - - - +
48C VAL* 2.7 42.9 + - - +
123C SER* 5.5 8.7 - - - -
124C GLU 5.1 5.6 - - - -
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Residues in contact with MET 40 (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 VAL* 3.9 13.4 - - - +
39C ALA* 1.3 81.7 - - - +
41C ASP* 1.3 70.6 + - - +
44C HIS* 4.0 37.4 - - + +
46C ALA 3.1 15.0 - - - +
47C LEU* 3.9 19.5 - - + -
124C GLU* 3.7 51.9 + - + +
126C LEU* 3.9 24.0 - - + -
122G ASP* 4.4 8.3 + - - +
147K MET* 4.1 9.4 - - - -
148K THR* 4.4 4.7 - - + -
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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