Contacts of the strand formed by residues 58 - 64 (chain A) in PDB entry 2MY9
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 ALA 58 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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36A LEU* 4.1 11.4 - - + -
37A ALA* 3.1 21.3 - - - +
39A PRO* 3.7 23.0 - - + +
57A SER* 1.3 73.5 - - - +
59A GLU* 1.3 59.3 + - - +
103A LYS* 3.2 8.7 - - - +
104A MET* 2.8 46.7 + - + +
105A LYS 4.0 4.5 - - - +
109A VAL* 5.4 2.2 - - + -
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Residues in contact with GLU 59 (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 LEU* 3.8 5.2 - - - -
37A ALA* 2.8 32.2 + - + +
57A SER 5.3 0.9 - - - +
58A ALA* 1.3 76.7 - - - +
60A VAL* 1.3 73.1 + - - +
61A LYS* 3.3 32.8 + - + +
101A GLY* 4.2 12.9 - - - +
102A GLN 3.4 14.6 - - - +
103A LYS* 2.8 38.5 + - + +
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Residues in contact with VAL 60 (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 ILE* 3.9 9.4 - - + -
35A HIS 3.4 7.6 - - - +
36A LEU* 3.9 16.4 - - + +
59A GLU* 1.3 74.3 - - - +
61A LYS* 1.3 65.9 + - - +
99A MET* 3.3 19.3 - - + +
100A VAL* 3.5 21.0 - - - +
101A GLY* 2.9 24.7 + - - -
102A GLN* 2.8 18.7 + - + +
104A MET* 4.0 11.2 - - + -
116A PHE* 3.4 43.1 - - + -
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Residues in contact with LYS 61 (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 ILE* 3.3 6.2 - - - +
35A HIS* 2.8 53.7 + - + +
37A ALA* 4.2 20.0 - - + +
59A GLU* 3.3 37.9 - - - +
60A VAL* 1.3 79.4 - - - +
62A ARG* 1.3 60.4 + - - +
63A GLU* 5.6 1.6 - - + -
100A VAL* 3.9 10.1 - - - -
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Residues in contact with ARG 62 (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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28A ILE* 3.9 23.6 - - + -
32A TYR* 3.5 38.8 - - + -
33A VAL 3.4 11.9 - - - +
34A ILE* 4.0 14.6 - - + -
61A LYS* 1.3 73.4 - - - +
63A GLU* 1.3 78.2 + - - +
97A LYS* 5.9 3.4 - - - +
100A VAL* 4.1 15.1 - - + +
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Residues in contact with GLU 63 (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* 3.5 13.0 - - - -
33A VAL* 2.8 37.8 + - - +
35A HIS* 3.4 22.0 + - + +
61A LYS* 5.6 2.0 - - + -
62A ARG* 1.3 83.0 - - - +
64A ARG* 1.3 64.8 + - - +
67A ASP* 3.9 22.4 - - - +
68A VAL* 3.6 13.7 - - + -
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Residues in contact with ARG 64 (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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31A GLY 3.5 10.3 - - - +
32A TYR* 3.2 42.1 + - + -
33A VAL* 4.1 0.9 - - - -
63A GLU* 1.3 81.9 + - - +
65A LEU* 1.3 64.9 + - - +
66A GLU* 4.5 11.4 - - + +
67A ASP* 3.1 17.8 + - + +
68A VAL* 2.9 22.2 + - - +
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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