Contacts of the strand formed by residues 34 - 39 (chain A) in PDB entry 3VI4
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 SER 34 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25A PHE* 3.6 2.9 - - - -
26A TYR* 2.7 46.3 + - - +
32A GLY 3.3 9.3 + - - -
33A VAL* 1.3 79.1 + - - +
35A VAL* 1.3 62.9 + - - +
57A LEU* 3.8 27.3 - - - +
58A CYS 3.2 16.6 - - - -
59A PRO* 3.2 15.2 - - - +
60A TRP* 4.2 2.5 - - - +
425A LEU* 4.6 5.0 - - - +
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Residues in contact with VAL 35 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11A LEU* 3.7 18.6 - - + -
24A GLU 3.4 2.5 - - - -
34A SER* 1.3 74.7 - - - +
36A LEU* 1.3 66.3 + - - +
37A VAL* 3.7 23.1 - - + -
56A TYR 3.7 0.5 - - - +
57A LEU* 4.0 0.5 - - - -
58A CYS* 2.8 39.1 + - - +
60A TRP* 5.1 7.4 - - + +
425A LEU* 3.9 20.4 - - + -
434A ILE* 3.7 35.2 - - + -
445A VAL* 3.7 19.7 - - + -
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Residues in contact with LEU 36 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22A SER 4.0 0.2 - - - +
23A VAL* 3.3 8.1 - - - +
24A GLU* 2.5 68.8 + - + +
26A TYR* 3.8 24.5 - - + -
35A VAL* 1.3 74.0 - - - +
37A VAL* 1.3 63.7 + - - +
38A GLY 4.2 0.4 - - - -
55A VAL* 4.7 1.8 - - + -
56A TYR 3.4 12.6 - - - +
57A LEU* 4.0 21.5 - - + -
70A ILE* 3.9 22.7 - - + -
105A VAL* 3.8 18.8 - - + +
107A ALA* 3.9 7.6 - - + -
112A ILE* 3.8 20.0 - - + -
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Residues in contact with VAL 37 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11A LEU* 4.3 1.6 - - + -
19A PHE* 3.5 38.6 - - + -
20A GLY* 3.3 36.6 - - - +
22A SER 3.8 3.1 - - - +
23A VAL* 4.8 2.5 - - + -
35A VAL* 3.7 19.3 - - + -
36A LEU* 1.3 79.4 - - - +
38A GLY* 1.3 61.5 + - - +
39A ALA 3.8 0.3 + - - -
55A VAL* 4.2 3.1 - - - +
56A TYR* 2.7 42.0 + - + +
58A CYS* 4.2 8.7 - - - -
443A ALA* 4.2 12.3 - - + -
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Residues in contact with GLY 38 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18A PHE 3.5 2.1 - - - +
20A GLY 3.0 25.6 + - - -
21A PHE 3.5 4.5 + - - -
22A SER* 3.1 14.3 + - - -
37A VAL* 1.3 72.8 - - - +
39A ALA* 1.3 59.7 + - - +
40A PRO* 3.9 5.2 - - - -
54A ALA 3.8 5.4 - - - -
55A VAL* 4.4 0.4 - - - -
102A GLY 3.3 20.6 - - - -
105A VAL* 3.8 14.5 - - - +
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Residues in contact with ALA 39 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17A SER* 3.2 21.8 - - - +
18A PHE 3.9 1.6 - - - -
19A PHE* 3.8 13.5 - - + -
37A VAL 3.8 0.2 + - - -
38A GLY* 1.3 73.3 - - - +
40A PRO* 1.3 61.7 - - - +
42A ALA* 3.1 15.7 + - + +
54A ALA 2.9 28.9 + - - +
56A TYR* 3.7 31.0 - - + -
102A GLY 4.2 0.6 + - - -
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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