Contacts of the strand formed by residues 44 - 49 (chain A) in PDB entry 1JV5
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 44 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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36A TYR* 4.2 16.2 - - + -
37A GLN 3.2 9.6 - - - +
38A GLN* 4.1 13.2 - - + -
43A THR* 1.3 78.2 - - - +
45A LYS* 1.3 71.5 + - - +
87A PHE* 6.2 2.0 - - + -
339B LEU* 6.4 0.2 - - + -
345B LEU* 6.3 1.6 - - + -
395B TYR* 3.6 37.2 - - + +
408B TRP* 3.6 64.6 + - + +
409B GLY 4.9 1.4 + - - -
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Residues in contact with LYS 45 (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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36A TYR* 3.3 10.9 - - - +
37A GLN* 2.8 63.2 + - + +
39A LYS* 2.8 39.3 - - - +
43A THR* 3.7 20.9 + - - +
44A VAL* 1.3 85.0 - - - +
46A LEU* 1.3 66.8 + - - +
47A LEU* 4.3 6.0 - - + +
406B ALA 6.0 0.4 - - - -
408B TRP* 5.1 1.8 - - - -
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Residues in contact with LEU 46 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34A ASN* 4.5 7.9 - - + -
35A TRP 3.4 8.3 - - - +
36A TYR* 3.9 22.6 - - + +
45A LYS* 1.3 74.7 - - - +
47A LEU* 1.3 71.4 + - - +
48A ILE 3.2 26.5 - - - +
49A HIS* 4.4 7.6 - - + -
55A HIS* 3.4 47.1 + - + +
58A VAL* 3.9 6.4 - - - +
403B LEU* 4.0 31.6 - - + -
405B PHE 4.1 14.8 + - - +
406B ALA* 4.8 8.1 + - - +
408B TRP* 5.2 1.0 - - - +
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Residues in contact with LEU 47 (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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35A TRP* 2.9 18.2 + - + +
36A TYR 4.3 1.6 - - - -
37A GLN* 3.3 50.3 - - + +
45A LYS* 4.3 4.9 - - + +
46A LEU* 1.3 76.8 - - - +
48A ILE* 1.3 64.1 + - + +
54A LEU* 3.7 0.7 - - - -
55A HIS* 2.7 34.2 + - - +
58A VAL* 3.6 32.8 - - + +
59A PRO* 5.6 0.9 - - + -
62A PHE* 4.2 17.7 - - + -
73A LEU* 5.1 4.7 - - + -
86A TYR* 3.6 24.7 - - + -
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Residues in contact with ILE 48 (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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33A LEU 5.0 0.2 - - - +
34A ASN* 3.4 0.7 - - - -
35A TRP* 2.9 37.9 + - + -
46A LEU* 3.2 9.9 - - - +
47A LEU* 1.3 84.3 - - + +
49A HIS* 1.3 65.7 + - - +
51A THR* 3.1 33.7 - - - +
52A SER* 3.7 3.8 - - - +
53A ARG 3.2 9.2 - - - +
54A LEU* 3.8 20.2 - - + -
62A PHE* 4.4 3.8 - - + -
63A SER* 3.6 10.3 - - - +
64A GLY* 3.5 25.4 - - - +
73A LEU* 3.5 30.3 - - + -
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Residues in contact with HIS 49 (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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33A LEU 3.9 1.1 - - - -
34A ASN* 3.1 16.8 - - - +
46A LEU* 4.4 15.6 - - + +
48A ILE* 1.3 75.2 - - - +
50A TYR* 1.3 81.6 + - + +
51A THR 3.1 3.1 + - - -
53A ARG* 2.8 59.2 + - + +
54A LEU 5.0 4.0 - - - -
55A HIS* 4.9 9.1 - + - -
403B LEU* 4.3 35.5 - - + +
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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