Contacts of the strand formed by residues 24 - 31 (chain F) in PDB entry 1VHA
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 VAL 24 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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19F LEU 3.5 0.3 - - - +
20F ILE* 3.4 4.3 - - - -
21F ILE 2.8 33.5 + - - +
22F GLY 3.6 10.1 - - - +
23F GLY* 1.3 84.9 - - - +
25F GLU* 1.3 76.6 + - - +
26F VAL* 3.6 11.0 + - + +
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Residues in contact with GLU 25 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18F PRO* 3.7 29.2 - - + +
19F LEU 3.2 12.3 - - - +
20F ILE* 4.4 10.7 - - + +
24F VAL* 1.3 82.2 - - - +
26F VAL* 1.3 68.3 + - - +
27F PRO* 4.6 2.9 - - + +
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Residues in contact with VAL 26 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18F PRO* 3.8 0.6 - - - +
19F LEU* 2.7 46.0 + - + +
21F ILE* 3.9 25.6 - - + +
24F VAL* 4.1 16.6 - - + +
25F GLU* 1.3 84.8 - - - +
27F PRO* 1.3 76.3 - - + +
28F TYR* 5.8 0.2 - - + -
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Residues in contact with PRO 27 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16F ASP* 5.3 9.2 - - + +
17F ARG 3.7 7.0 - - - +
18F PRO* 4.7 2.5 - - + -
25F GLU* 4.6 2.5 - - + +
26F VAL* 1.3 93.7 - - + +
28F TYR* 1.3 61.4 + - - +
29F HIS 4.2 0.6 + - - -
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Residues in contact with TYR 28 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15F GLU 3.7 0.5 - - - +
16F ASP* 3.3 5.7 - - - -
17F ARG* 2.9 43.2 + - + +
19F LEU* 3.5 38.6 - - + -
26F VAL* 5.8 0.2 - - + -
27F PRO* 1.3 75.7 - - - +
29F HIS* 1.3 75.5 + - - +
30F THR* 3.6 17.3 + - - -
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Residues in contact with HIS 29 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14F GLY* 3.9 4.7 - - - -
15F GLU 3.4 16.7 + - - -
16F ASP* 3.1 26.5 + - - +
27F PRO* 4.2 0.8 - - - +
28F TYR* 1.3 87.6 - - - +
30F THR* 1.3 70.0 + - - +
31F GLY 3.3 20.4 + - - +
32F PHE 2.5 26.8 + - - -
33F ILE* 3.4 31.4 - - + +
34F ALA* 4.5 12.6 - - + -
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Residues in contact with THR 30 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14F GLY* 3.2 4.9 - - - -
15F GLU* 2.7 59.8 + - + +
17F ARG* 4.8 10.2 + - - -
28F TYR* 3.6 21.7 + - + -
29F HIS* 1.3 74.4 + - - +
31F GLY* 1.3 66.0 + - - +
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Residues in contact with GLY 31 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13F PHE 4.3 7.2 - - - -
15F GLU* 4.3 5.4 - - - -
29F HIS* 3.3 10.8 + - - +
30F THR* 1.3 78.8 - - - +
32F PHE* 1.3 69.0 - - - -
33F ILE* 3.3 6.6 + - - +
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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