Contacts of the strand formed by residues 33 - 38 (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 LEU 33 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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4A MET* 3.5 30.1 - - + -
23A CYS* 4.2 1.8 - - - -
29A ILE* 3.9 14.1 - - + -
31A ASN 2.9 6.1 + - - -
32A TYR* 1.3 73.2 - - - +
34A ASN* 1.3 66.3 + - - +
35A TRP* 3.2 40.7 - - + +
48A ILE 4.8 0.3 - - - -
49A HIS* 3.7 1.0 - - - -
50A TYR* 3.2 5.3 + - - +
51A THR* 2.8 32.0 + - - +
71A TYR* 3.8 37.2 - - + -
88A CYS* 4.1 4.7 - - + -
89A GLN 3.4 20.0 - - - +
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Residues in contact with ASN 34 (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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32A TYR* 4.9 1.3 + - - -
33A LEU* 1.3 77.9 + - - +
35A TRP* 1.3 63.0 + - - +
36A TYR* 3.9 23.8 + - + +
46A LEU* 4.5 3.6 - - + -
48A ILE 3.4 8.5 - - - +
49A HIS* 3.1 12.3 - - - +
50A TYR 3.1 24.3 + - - -
87A PHE 3.8 0.5 - - - +
88A CYS* 3.2 5.2 - - - -
89A GLN* 2.8 58.5 + - - +
91A GLY* 4.9 8.1 - - - +
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Residues in contact with TRP 35 (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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6A GLN* 4.4 5.6 - - - -
21A ILE* 3.4 39.0 - - + -
23A CYS* 3.5 26.9 - - + -
33A LEU* 3.2 24.0 - - + +
34A ASN* 1.3 73.8 - - - +
36A TYR* 1.3 61.5 + - - +
46A LEU* 3.4 6.6 - - - +
47A LEU* 2.9 29.9 + - + -
48A ILE* 2.9 36.0 + - + +
51A THR* 4.6 5.7 + - - +
65A SER 5.7 0.2 + - - -
71A TYR* 4.3 0.8 - - - +
72A SER* 3.6 35.2 + - - +
73A LEU* 3.7 35.6 - - + +
86A TYR* 4.6 7.2 - - + -
87A PHE 3.4 12.8 - - - -
88A CYS* 3.7 21.3 - - + -
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Residues in contact with TYR 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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34A ASN* 3.9 21.0 + - + +
35A TRP* 1.3 73.5 - - - +
37A GLN* 1.3 61.0 + - - +
44A VAL* 4.2 10.3 - - + -
45A LYS 3.3 15.0 - - - +
46A LEU* 3.9 16.8 - - + +
47A LEU* 4.3 2.9 - - - -
85A THR 4.0 0.4 - - - +
86A TYR* 3.3 8.5 - - - +
87A PHE* 2.8 49.9 + - + +
89A GLN* 2.8 42.8 + - + -
98A PHE* 4.0 14.8 - + - -
345B LEU* 6.0 2.0 - - + -
405B PHE* 3.2 46.6 + + + +
408B TRP* 3.7 21.8 - + + -
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Residues in contact with GLN 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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36A TYR* 1.3 74.0 - - - +
38A GLN* 1.3 64.2 + - - +
39A LYS* 3.4 18.3 - - - +
43A THR 3.6 1.0 - - - +
44A VAL* 3.2 5.4 - - - -
45A LYS* 2.8 64.1 + - - +
47A LEU* 3.3 30.4 - - + +
62A PHE* 4.3 11.7 - - - -
81A GLU 4.3 8.1 + - - -
82A ASP* 4.7 1.6 + - - +
84A ALA* 4.0 14.9 - - + +
85A THR 3.6 4.0 - - - -
86A TYR* 3.4 27.8 + - + -
87A PHE* 5.5 0.4 - - - -
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Residues in contact with GLN 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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37A GLN* 1.3 72.3 - - - +
39A LYS* 1.3 70.7 + - - +
42A GLY* 4.5 6.8 + - - +
43A THR 3.2 9.4 - - - +
44A VAL* 4.1 9.9 - - + +
84A ALA* 3.1 18.1 - - - +
85A THR* 2.9 31.4 + - - +
87A PHE* 3.7 25.8 - - + -
339B LEU* 3.8 20.3 - - - +
393B LEU* 4.0 7.5 - - - +
395B TYR* 2.7 29.6 + - - +
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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