Contacts of the strand formed by residues 28 - 34 (chain B) in PDB entry 1V0O
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 THR 28 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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20B LYS* 3.8 26.0 + - + +
21B ALA 3.3 7.4 - - - +
22B GLN* 3.3 18.7 + - - +
26B GLY 4.0 2.3 + - - -
27B GLU* 1.3 70.5 - - - +
29B PHE* 1.3 75.5 + - - +
80B GLU* 5.4 0.3 - - - -
81B HIS* 3.4 42.3 + - + +
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Residues in contact with PHE 29 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4B TYR* 4.2 16.6 - + + -
19B TYR 3.6 0.7 - - - +
20B LYS* 3.7 2.8 - - - -
21B ALA* 2.9 33.7 + - - +
23B ASN* 3.4 33.9 - - - -
27B GLU* 3.4 29.8 - - + -
28B THR* 1.3 78.6 - - - +
30B ALA* 1.3 61.6 + - - +
31B LEU* 4.0 3.3 + - + -
66B TYR* 3.6 40.6 - + + -
78B VAL* 3.9 20.2 - - + -
79B PHE 3.4 8.7 - - - +
80B GLU* 4.8 1.1 - - - -
81B HIS* 3.7 9.3 - - - +
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Residues in contact with ALA 30 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18B VAL* 4.1 8.3 - - + -
19B TYR 3.2 9.0 - - - +
29B PHE* 1.3 72.4 - - - +
31B LEU* 1.3 60.9 + - - +
77B LEU 3.7 1.4 - - - +
78B VAL* 3.6 1.6 - - - -
79B PHE* 2.8 39.7 + - + +
80B GLU 3.7 4.5 - - - +
81B HIS* 3.7 8.1 - - - +
2638B INR 3.2 45.3 - - + +
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Residues in contact with LEU 31 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4B TYR* 3.9 36.1 - - + -
7B LEU* 3.5 25.6 - - + -
17B VAL 3.5 2.3 - - - +
18B VAL* 3.2 5.3 - - - -
19B TYR* 2.8 47.9 + - + +
21B ALA* 4.0 13.9 - - + -
29B PHE* 4.7 2.9 - - + -
30B ALA* 1.3 77.9 - - - +
32B LYS* 1.3 59.4 + - - +
33B LYS 3.8 0.4 - - - +
76B VAL* 3.9 17.9 - - + -
77B LEU 3.4 2.5 - - - -
78B VAL* 3.7 34.1 - - + -
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Residues in contact with LYS 32 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13B GLY* 5.0 6.7 - - - -
14B THR* 5.6 1.1 - - - +
15B TYR 5.4 5.8 - - - +
16B GLY* 5.0 6.7 - - - +
17B VAL 3.4 5.4 - - - +
18B VAL* 4.4 9.4 - - + +
30B ALA 4.1 0.4 + - - -
31B LEU* 1.3 70.5 - - - +
33B LYS* 1.3 66.9 + - - +
34B ILE* 3.3 27.5 + - + +
50B GLU* 3.2 29.3 + - - +
75B LEU 3.8 0.2 - - - +
76B VAL* 3.5 3.6 - - - -
77B LEU* 2.8 36.7 + - + +
79B PHE* 3.7 25.8 - - + -
143B ASP* 4.0 12.1 + - - +
2638B INR 2.6 42.9 + - + +
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Residues in contact with LYS 33 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16B GLY* 3.2 5.5 - - - -
17B VAL* 2.9 41.2 + - + +
19B TYR* 3.9 25.7 - - + +
31B LEU* 3.7 2.6 + - - +
32B LYS* 1.3 69.1 - - - +
34B ILE* 1.3 81.8 + - - +
35B ARG* 3.4 21.7 + - - +
36B LEU* 5.3 1.2 - - - +
74B ARG* 4.0 46.0 - - + +
75B LEU 3.8 8.3 - - - +
76B VAL* 4.7 9.8 - - + +
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Residues in contact with ILE 34 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15B TYR* 3.9 13.9 - - + +
32B LYS* 3.9 33.0 - - + +
33B LYS* 1.3 79.3 + - - +
35B ARG* 1.3 67.4 + - - +
36B LEU* 3.1 23.6 + - + +
47B THR* 4.0 21.5 - - + +
50B GLU* 5.7 2.2 - - - +
74B ARG* 5.8 0.2 - - - -
75B LEU* 3.0 49.8 + - + +
77B LEU* 4.1 23.8 - - + -
155B ARG* 5.9 4.0 - - - +
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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