Contacts of the strand formed by residues 45 - 49 (chain M) in PDB entry 3KYM
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 45 (chain M).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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36M TYR* 3.1 9.7 - - - -
37M GLN* 2.8 65.3 + - + +
39M LYS* 2.8 28.0 - - - +
43M ALA 5.4 0.4 - - - +
44M PRO* 1.3 77.8 - - - +
46M LEU* 1.3 64.9 + - - +
47M LEU* 3.9 4.9 - - - +
58M ILE* 3.4 31.2 - - - +
59M PRO* 4.3 17.6 - - - +
61M ARG* 6.2 0.2 - - - +
62M PHE* 5.1 3.0 - - - -
81M GLU* 5.9 1.2 + - - -
109N TRP* 4.2 8.3 - - + -
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Residues in contact with LEU 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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34M ALA* 3.9 5.2 - - + -
35M TRP 3.2 18.6 - - - +
36M TYR* 3.5 29.4 - - + +
45M ARG* 1.3 77.5 - - - +
47M LEU* 1.3 59.6 + - - +
48M ILE 3.5 16.2 - - - +
49M TYR* 4.2 10.1 - - + -
55M ALA* 3.9 25.7 - - + +
58M ILE* 3.4 22.5 - - - +
105N TYR* 3.5 33.0 - - + -
106N PHE 3.6 12.8 - - - +
107N ASP* 4.3 13.8 - - + +
109N TRP* 4.3 4.0 - - - +
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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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35M TRP* 3.1 10.9 + - + +
36M TYR 4.2 3.8 - - - +
37M GLN* 3.8 29.8 - - + +
45M ARG* 3.9 18.2 - - - +
46M LEU* 1.3 80.2 - - - +
48M ILE* 1.3 70.5 + - + +
54M ARG* 3.2 9.0 - - - -
55M ALA 3.0 22.0 + - - -
58M ILE* 3.8 27.5 - - + +
62M PHE* 4.0 23.6 - - + -
73M LEU* 4.5 9.9 - - + -
86M TYR* 3.8 33.9 - - + -
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Residues in contact with ILE 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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33M LEU 5.2 0.2 - - - +
34M ALA* 2.9 9.2 - - - +
35M TRP* 2.9 46.5 + - + +
46M LEU* 3.5 6.3 - - - +
47M LEU* 1.3 90.0 - - + +
49M TYR* 1.3 63.3 + - - +
51M ALA 3.4 19.7 - - - +
52M SER 3.7 11.0 - - - +
53M ASN 2.9 33.7 - - - +
54M ARG* 4.2 10.1 - - + +
55M ALA 4.5 0.2 - - - +
62M PHE* 4.8 2.0 - - + +
63M SER* 3.7 10.5 - - - -
64M GLY 3.2 29.4 - - - +
73M LEU* 4.5 7.2 - - + -
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Residues in contact with TYR 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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33M LEU 3.8 2.7 - - - -
34M ALA* 4.4 1.6 - - - +
46M LEU* 4.2 6.5 - - + -
48M ILE* 1.3 74.7 - - - +
50M ASP* 1.3 83.2 + - - +
51M ALA 3.4 2.7 - - - -
53M ASN* 2.8 71.6 + - + +
54M ARG 4.7 3.1 - - - -
55M ALA* 4.5 17.3 - - + -
91M TYR* 4.4 0.4 - - - -
103N ASP* 5.0 2.0 - - - -
105N TYR* 3.5 51.6 - + + -
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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