Contacts of the strand formed by residues 92 - 96 (chain L) 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 ALA 92 (chain L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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38L ARG* 3.8 35.9 - - + +
39L GLN 3.9 4.3 - - - -
40L ALA* 3.8 16.8 - - + +
41L PRO* 4.5 3.1 - - - -
90L ASP 3.0 10.8 + - - +
91L THR* 1.3 76.6 - - - +
93L THR* 1.3 63.0 + - - +
94L TYR* 3.5 11.6 - - + -
114L LEU* 5.5 2.0 - - - -
115L VAL 3.1 28.1 + - - +
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Residues in contact with THR 93 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38L ARG* 3.2 7.8 - - - +
39L GLN* 2.9 52.9 + - - +
41L PRO* 5.5 0.4 - - - +
92L ALA* 1.3 73.3 - - - +
94L TYR* 1.3 60.1 + - - +
95L TYR* 4.0 20.5 + - - +
112L GLY* 5.5 1.1 - - - -
113L THR 3.2 14.6 - - - +
114L LEU* 4.2 24.0 - - + -
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Residues in contact with TYR 94 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6L GLU* 3.7 6.6 - - - +
20L LEU* 4.2 12.3 - - + -
36L TRP* 4.5 11.2 - + + -
37L VAL 3.3 9.2 - - - -
38L ARG* 3.5 41.4 + - + -
48L VAL* 4.9 6.5 - - + -
68L PHE* 4.3 7.2 - + - -
81L LEU* 4.7 13.0 - - + -
83L MET* 4.1 20.1 - - - +
90L ASP* 2.9 26.4 + - - +
92L ALA* 3.5 24.2 - - + -
93L THR* 1.3 70.4 - - - +
95L TYR* 1.3 63.7 + - - +
112L GLY* 3.6 2.4 - - - -
113L THR* 2.8 45.6 + - + +
115L VAL* 3.9 28.9 - - + -
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Residues in contact with TYR 95 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38K GLN* 3.4 11.8 + - - -
42K GLN 4.2 2.6 + - - -
43K ALA* 3.7 29.6 - - + -
44K PRO* 3.8 11.4 - - + -
6L GLU* 4.1 3.4 - - - +
36L TRP* 3.4 3.6 - - - -
37L VAL* 2.5 50.8 + - + +
39L GLN* 3.4 39.1 + - + -
45L LEU* 4.4 6.3 - - + -
93L THR* 4.0 19.1 + - - +
94L TYR* 1.3 72.6 - - - +
96L CYS* 1.3 61.4 + - - +
109L TRP* 3.5 33.2 - + + -
110L GLY 4.1 2.9 - - - +
111L ARG 4.3 1.8 - - - -
112L GLY* 3.6 28.5 - - - -
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Residues in contact with CYS 96 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4L LEU* 3.6 14.1 - - - +
6L GLU* 2.9 19.7 + - - +
22L CYS* 2.1 51.4 - - + -
34L MET* 3.8 9.4 - - - -
35L PHE 3.5 10.3 - - - +
36L TRP* 3.5 14.5 - - + -
79L LEU* 4.3 0.9 - - + -
95L TYR* 1.3 75.1 - - - +
97L ALA* 1.3 61.5 + - - +
109L TRP* 3.8 1.4 - - - -
110L GLY 3.3 21.7 + - - -
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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