Contacts of the strand formed by residues 43 - 49 (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 VAL 43 (chain M).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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37M ARG 3.6 3.1 - - - +
38M LYS* 3.9 24.0 - - + +
42M HIS* 1.3 82.4 - - - +
44M ARG* 1.3 60.7 + - - +
62M HIS* 4.8 0.7 - - - -
63M SER* 3.0 33.2 + - - -
75M THR 4.6 6.1 - - - +
76M GLY* 5.5 1.1 - - - -
77M ASN 5.2 0.9 - - - +
81M ALA* 3.7 33.4 - - + +
84M THR* 3.3 15.8 - - + +
114M LYS* 4.5 14.6 - - + +
118M ILE* 3.6 23.6 - - + -
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Residues in contact with ARG 44 (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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49 G 2.7 65.1 + - - +
59 G 3.4 20.2 + - - +
1209 A 4.1 15.2 + - - -
35M VAL 3.5 1.1 - - - +
36M ALA* 3.7 2.1 - - - -
37M ARG* 2.8 44.4 + - + +
42M HIS 4.4 0.2 - - - -
43M VAL* 1.3 74.3 - - - +
45M ALA* 1.3 66.1 + - - +
46M GLN* 3.9 35.4 - - + +
60M SER* 5.5 2.2 - - - -
61M ALA 3.7 8.7 - - - +
62M HIS* 3.8 34.3 + - + +
84M THR* 4.6 0.4 - - - -
118M ILE* 4.0 3.6 - - - +
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Residues in contact with ALA 45 (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* 4.7 6.1 - - + -
35M VAL 3.4 5.4 - - - +
44M ARG* 1.3 77.3 - - - +
46M GLN* 1.3 60.8 + - - +
60M SER* 3.1 4.3 - - - -
61M ALA 2.9 36.9 + - - +
84M THR* 4.1 13.2 - - + +
85M GLY* 4.5 1.3 - - - -
88M ALA* 3.6 21.5 - - + +
118M ILE* 3.9 25.1 - - + -
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Residues in contact with GLN 46 (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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49 G 4.4 0.6 - - - +
59 G 2.6 62.3 + - - +
69 C 3.9 4.8 - - - +
1199 C 4.0 7.1 + - - -
33M ARG 3.2 1.0 - - - +
34M LEU* 3.4 4.4 - - - +
35M VAL* 2.7 50.6 + - + +
44M ARG* 3.9 21.5 - - + +
45M ALA* 1.3 77.4 - - - +
47M LEU* 1.3 62.8 + - - +
48M VAL* 3.7 9.4 - - + -
57M THR* 3.8 15.9 + - + +
59M ALA 3.4 4.3 - - - -
60M SER* 3.6 17.7 - - - +
88M ALA* 5.9 0.4 - - - -
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Residues in contact with LEU 47 (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* 5.3 4.7 - - + -
33M ARG 3.4 4.3 - - - +
34M LEU* 3.4 46.2 - - + +
46M GLN* 1.3 70.9 - - - +
48M VAL* 1.3 61.7 + - - +
57M THR* 3.6 0.9 - - - -
58M LEU* 3.0 29.3 + - + +
59M ALA* 2.8 21.9 + - + +
88M ALA* 5.3 4.0 - - + +
92M ALA* 3.2 34.1 - - + -
97M VAL* 3.4 31.2 - - + -
100M ALA* 3.9 10.8 - - + -
127M LEU* 3.4 11.7 - - + -
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Residues in contact with VAL 48 (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 3.8 12.3 - - + +
32M PRO* 3.5 5.3 - - - +
33M ARG* 2.8 48.9 + - - +
35M VAL* 3.7 24.5 - - + -
46M GLN* 3.9 11.4 - - + -
47M LEU* 1.3 76.8 - - - +
49M THR* 1.3 65.1 + - - +
55M ASP* 3.1 41.1 - - + +
56M ASP 3.4 10.1 - - - +
57M THR* 3.7 17.0 - - - +
58M LEU* 4.9 0.2 - - - -
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Residues in contact with THR 49 (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* 4.9 15.1 - - - +
33M ARG* 6.1 0.2 - - - -
48M VAL* 1.3 78.7 - - - +
50M LEU* 1.3 68.8 + - - +
55M ASP* 3.4 6.9 - - - +
56M ASP* 2.7 55.7 + - + +
58M LEU* 3.4 24.3 - - + +
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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