Contacts of the strand formed by residues 35 - 38 (chain O) 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 TRP 35 (chain O).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6O GLN* 3.3 24.5 - - - -
21O LEU* 4.4 10.1 - - + -
22O SER 4.0 2.9 - - - -
23O CYS* 3.1 43.5 - - + -
33O LEU* 4.1 2.8 - - + +
34O ALA* 1.3 81.8 - - - +
36O TYR* 1.3 62.7 + - - +
46O LEU* 3.6 2.4 - - - +
47O LEU* 2.7 45.5 + - + -
48O ILE* 3.5 28.1 + - + +
64O GLY* 5.4 0.7 - - - -
71O PHE* 3.3 38.0 - + + -
72O THR 3.9 10.0 + - - -
73O LEU* 4.0 38.6 - - + -
86O TYR* 4.9 4.3 - - + -
87O TYR 3.3 19.1 - - - -
88O CYS* 4.1 7.4 - - + -
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Residues in contact with TYR 36 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34O ALA* 4.3 7.9 - - + -
35O TRP* 1.3 76.6 - - - +
37O GLN* 1.3 60.9 + - - +
38O GLN 3.9 0.2 + - - -
44O PRO* 4.3 11.4 - - + -
45O ARG 3.2 17.5 - - - +
46O LEU* 3.7 15.3 - - + -
47O LEU* 3.9 4.3 - - - -
85O VAL 3.7 0.5 - - - +
86O TYR* 3.3 8.3 - - - +
87O TYR* 3.0 47.7 + - + +
89O GLN* 2.5 51.3 + - + -
98O PHE* 4.5 9.6 - + - -
45P LEU* 5.2 2.0 - - + -
105P TYR* 3.8 3.8 - - - +
106P PHE* 2.9 42.8 + + - -
109P TRP* 3.7 26.2 - + - -
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Residues in contact with GLN 37 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36O TYR* 1.3 73.2 - - - +
38O GLN* 1.3 61.2 + - - +
39O LYS* 2.9 41.1 + - + +
43O ALA 4.1 1.2 - - - +
44O PRO* 3.4 2.1 - - - +
45O ARG* 2.9 63.9 + - + +
47O LEU* 3.7 17.6 - - + +
62O PHE* 4.2 5.3 - - - -
81O GLU 3.7 9.7 + - - -
82O ASP* 4.0 11.9 + - - -
84O ALA* 4.3 3.6 - - + +
85O VAL 3.7 2.7 - - - -
86O TYR* 3.3 40.9 + - + -
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Residues in contact with GLN 38 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36O TYR 3.9 0.2 + - - -
37O GLN* 1.3 72.7 - - - +
39O LYS* 1.3 63.7 + - - +
40O PRO* 3.6 2.7 - - + +
41O GLY 5.7 1.1 - - - +
42O GLN 3.6 24.4 + - - +
43O ALA 4.3 5.2 - - - +
44O PRO* 4.1 22.6 - - + +
84O ALA* 3.4 3.7 - - - +
85O VAL* 2.8 38.5 + - + +
87O TYR* 3.5 23.4 + - + -
39P GLN* 2.9 39.0 + - - +
45P LEU* 4.7 0.2 - - - +
95P TYR* 3.7 13.9 + - - -
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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