Contacts of the strand formed by residues 33 - 38 (chain M) in PDB entry 1JJ2
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 ARG 33 (chain M).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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69 C 2.8 30.4 + - - -
79 G 3.3 17.4 + - - -
23M ARG* 3.8 13.4 - - - +
26M LEU* 4.1 26.5 - - + +
27M LEU* 4.2 18.4 - - + +
31M LYS 4.6 5.4 - - - +
32M PRO* 1.3 75.0 - - - +
34M LEU* 1.3 59.7 + - - +
35M VAL* 3.4 9.3 + - + +
46M GLN 3.2 2.1 - - - +
47M LEU* 3.2 8.3 - - - -
48M VAL* 2.8 48.7 + - - +
55M ASP* 2.8 24.9 + - - -
101M VAL* 3.4 10.8 - - + +
103M ASP* 2.5 47.2 + - + -
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Residues in contact with LEU 34 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32M PRO 4.0 0.4 + - - -
33M ARG* 1.3 68.7 - - - +
35M VAL* 1.3 60.8 + - - +
36M ALA 3.3 1.0 + - - -
45M ALA* 4.7 16.8 - - + -
46M GLN 4.0 6.7 - - - +
47M LEU* 3.4 25.4 - - + -
88M ALA* 5.5 5.2 - - + -
89M GLY 6.1 0.4 - - - +
100M ALA* 4.1 7.4 - - + +
101M VAL 2.8 15.0 + - - +
102M LEU* 3.6 17.3 - - + +
103M ASP 2.9 24.1 + - - +
118M ILE* 4.5 7.6 - - + +
119M GLN* 4.1 18.4 - - + +
122M ALA* 3.6 23.8 - - + -
127M LEU* 5.2 0.9 - - + -
129M ILE* 3.5 24.9 - - + -
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Residues in contact with VAL 35 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69 C 3.7 31.6 - - - -
33M ARG* 4.0 30.1 - - + +
34M LEU* 1.3 69.4 - - - +
36M ALA* 1.3 58.6 + - - +
37M ARG* 3.7 21.9 + - + +
44M ARG 3.5 2.6 - - - +
45M ALA* 3.4 6.6 - - - -
46M GLN* 2.7 45.7 + - + +
48M VAL* 3.7 26.2 - - + -
103M ASP* 3.5 6.5 - - - +
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Residues in contact with ALA 36 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34M LEU 3.3 1.2 + - - -
35M VAL* 1.3 71.2 - - - +
37M ARG* 1.3 74.7 + - - +
44M ARG 3.7 4.5 - - - -
102M LEU* 3.9 24.0 - - + -
103M ASP 2.9 13.1 + - - +
104M ILE* 4.0 4.2 - - - -
107M ASN* 3.9 8.7 - - - +
115M VAL* 4.0 17.3 - - + +
118M ILE* 3.7 28.7 - - + -
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Residues in contact with ARG 37 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59 G 3.7 24.9 - - - +
69 C 2.2 64.2 + - - -
79 G 4.7 4.4 + - - -
17M ARG 5.2 1.9 + - - -
35M VAL* 3.7 17.4 + - + +
36M ALA* 1.3 86.2 + - - +
38M LYS* 1.3 66.4 + - - +
43M VAL* 3.6 4.3 - - - +
44M ARG* 2.8 47.3 + - + +
103M ASP* 3.0 33.7 + - - -
104M ILE 3.9 0.2 - - - -
105M GLY* 3.1 24.8 - - - +
106M LEU 5.6 0.4 - - - +
107M ASN* 4.2 2.2 - - - -
118M ILE* 4.4 1.1 - - - +
8507M CL 3.3 21.1 - - + -
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Residues in contact with LYS 38 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59 G 6.0 2.4 - - - +
289 U 4.3 4.0 + - - -
479 A 4.3 12.5 + - - -
489 C 2.7 28.8 + - - +
146D LYS* 3.8 10.1 + - - +
37M ARG* 1.3 81.1 - - - +
39M SER* 1.3 66.3 + - - +
42M HIS 3.6 7.0 - - - +
43M VAL* 3.9 13.7 - - + +
107M ASN* 3.3 28.6 - - - +
114M LYS* 3.6 34.7 - - + +
115M VAL* 4.6 16.8 - - + -
118M ILE* 5.3 1.6 - - + -
8507M CL 3.4 17.5 - - - +
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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