Contacts of the strand formed by residues 46 - 53 (chain B) in PDB entry 2JJ6
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 46 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33B SER* 3.9 8.3 - - - +
34B LEU 3.6 6.5 - - - +
35B THR* 3.5 17.7 - - + -
43B PRO* 6.4 0.7 - - + -
44B ALA 3.8 7.6 - - - +
45B ASP* 1.3 72.7 - - - +
47B ALA* 1.3 63.8 + - - +
48B ILE 3.5 28.7 - - - +
49B GLU* 3.8 21.3 - - + +
62B ASN 4.3 3.1 - - - +
63B SER* 3.2 5.1 - - - -
64B CYS* 2.8 50.9 + - + +
69B ARG* 6.0 1.1 - - - +
114B ILE* 3.8 5.2 - - - +
124B LYS* 6.1 0.4 - - - +
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Residues in contact with ALA 47 (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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34B LEU* 2.8 13.3 + - + +
35B THR* 4.3 0.2 - - - +
36B CYS* 5.1 1.1 - - - -
45B ASP 4.0 1.0 + - - -
46B VAL* 1.3 72.3 - - - +
48B ILE* 1.3 60.6 + - - +
63B SER* 3.5 9.7 - - - -
98B PHE* 4.4 9.9 - - + -
110B PHE* 3.3 21.1 - - - -
113B ARG* 5.1 3.1 + - - +
114B ILE* 3.6 23.0 + - + +
120B ILE* 3.6 42.2 - - + -
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Residues in contact with ILE 48 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32B ILE 4.7 0.2 - - - -
33B SER* 2.9 7.2 - - - -
34B LEU* 2.9 60.9 + - + +
46B VAL* 3.5 3.1 - - - +
47B ALA* 1.3 80.9 - - - +
49B GLU* 1.3 65.0 + - - +
50B LEU* 3.8 28.0 - - + -
62B ASN 3.5 4.3 - - - -
91B ILE* 5.0 7.0 - - + -
98B PHE* 3.9 24.0 - - + -
100B VAL* 4.3 9.2 - - + -
108B PHE* 5.0 0.2 - - + -
110B PHE* 3.7 43.1 - - + -
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Residues in contact with GLU 49 (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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31B ALA* 4.7 12.6 - - + +
32B ILE 4.7 0.4 - - - +
33B SER* 3.6 14.0 + - - +
46B VAL* 3.8 16.7 - - + +
48B ILE* 1.3 73.8 - - - +
50B LEU* 1.3 69.0 + - - +
51B LYS* 4.6 13.4 - - - +
60B LEU 3.3 1.4 - - - +
61B ARG* 2.9 31.9 - - - +
62B ASN* 2.8 19.4 + - - +
69B ARG* 3.1 39.9 + - - +
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Residues in contact with LEU 50 (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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30B PHE* 3.8 3.1 - - - +
31B ALA* 3.3 4.5 - - - -
32B ILE* 2.6 51.1 + - + +
48B ILE* 3.8 26.2 - - + -
49B GLU* 1.3 75.4 - - - +
51B LYS* 1.3 60.3 + - - +
52B ALA* 4.1 0.4 - - - +
59B LEU* 4.6 12.7 - - + +
60B LEU 3.7 2.0 - - - -
61B ARG* 3.9 5.2 - - + -
81B PHE* 6.4 2.5 - - + -
89B VAL* 4.2 11.2 - - + -
91B ILE* 4.2 20.2 - - + -
100B VAL* 3.8 24.9 - - + -
108B PHE* 3.5 29.6 - - + -
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Residues in contact with LYS 51 (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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29B SER* 3.0 44.3 + - - -
30B PHE 3.9 6.0 - - - +
31B ALA* 3.9 19.6 - - + +
49B GLU* 3.8 14.8 - - - +
50B LEU* 1.3 72.4 - - - +
52B ALA* 1.3 61.9 + - - +
53B VAL* 3.7 16.1 + - + -
58B GLN 3.5 1.4 - - - +
59B LEU* 3.1 5.5 - - - +
60B LEU* 2.7 55.8 + - + +
126B ASN* 5.5 4.9 - - - +
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Residues in contact with ALA 52 (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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29B SER* 2.9 26.9 - - - -
30B PHE* 3.1 39.2 + - + +
50B LEU 4.0 0.6 + - - +
51B LYS* 1.3 73.3 - - - +
53B VAL* 1.3 60.7 + - - +
54B PHE* 3.6 4.4 - - - -
58B GLN 3.2 5.6 - - - -
59B LEU* 3.8 7.0 - - + -
79B PHE* 3.7 9.6 - - + -
81B PHE* 3.7 20.9 - - + -
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Residues in contact with VAL 53 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28B GLU 3.8 12.3 - - - +
29B SER* 4.3 6.5 - - - -
51B LYS* 4.0 22.7 - - + +
52B ALA* 1.3 70.8 - - - +
54B PHE* 1.3 58.8 + - - +
55B THR* 4.4 10.3 - - - +
56B ASP* 4.6 13.5 - - + +
57B ARG 3.0 6.2 + - - -
58B GLN* 2.6 47.8 + - + +
60B LEU* 4.3 18.2 - - + -
79B PHE* 4.2 1.3 - - - -
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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