Contacts of the strand formed by residues 85 - 90 (chain K) 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 VAL 85 (chain K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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36K TYR 3.7 0.3 - - - +
37K GLN* 3.6 2.4 - - - -
38K GLN* 2.8 43.9 + - + +
84K ALA* 1.3 78.8 - - - +
86K TYR* 1.3 68.9 + - - +
87K TYR* 3.4 42.0 - - + +
100K GLY 5.4 0.2 - - - +
101K GLY* 4.2 7.4 - - - -
102K THR 3.7 7.4 - - - +
103K LYS* 4.1 28.9 - - + +
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Residues in contact with TYR 86 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6K GLN* 2.8 23.1 + - - +
21K LEU* 3.7 25.4 - - + -
35K TRP* 4.5 9.4 - - + -
36K TYR 3.3 13.5 - - - +
37K GLN* 2.8 40.2 + - + -
47K LEU* 4.0 5.2 - - + -
62K PHE* 3.9 16.0 - + - -
73K LEU* 3.6 16.8 - - + -
75K ILE* 3.7 13.0 - - + +
82K ASP* 2.7 37.8 + - - +
84K ALA* 3.7 13.7 - - + -
85K VAL* 1.3 77.4 - - - +
87K TYR* 1.3 56.0 + - - +
101K GLY* 3.3 3.6 - - - -
102K THR* 3.2 18.3 + - - +
104K VAL* 3.7 18.4 - - + -
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Residues in contact with TYR 87 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6K GLN* 3.3 6.5 - - - +
35K TRP* 3.6 6.2 - - - -
36K TYR* 3.0 44.6 + - + +
38K GLN* 3.6 24.8 + - + -
44K PRO* 5.6 0.7 - - + -
85K VAL* 3.4 30.3 - - + +
86K TYR* 1.3 74.8 - - - +
88K CYS* 1.3 65.2 + - - +
98K PHE* 4.6 6.1 - - + -
99K GLY 4.3 7.4 - - - -
100K GLY 3.8 18.4 - - - -
101K GLY* 3.8 16.6 - - - -
39L GLN* 2.9 25.3 + - - -
43L LYS 4.1 2.4 + - - -
44L GLY* 3.9 15.4 - - - -
45L LEU* 3.6 31.9 - - + -
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Residues in contact with CYS 88 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4K MET* 4.0 22.2 - - - -
6K GLN* 3.4 8.6 + - - -
23K CYS* 2.0 49.6 - - + -
33K LEU* 3.7 17.7 - - + -
34K ALA 3.3 5.4 - - - -
35K TRP* 3.8 13.5 - - + -
87K TYR* 1.3 76.0 - - - +
89K GLN* 1.3 63.4 + - - +
98K PHE* 3.3 5.9 - - - +
99K GLY 2.9 24.0 + - - -
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Residues in contact with GLN 89 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4K MET* 5.2 0.4 - - - -
33K LEU* 3.2 11.9 - - - +
34K ALA* 2.9 29.3 + - - +
36K TYR* 2.5 41.2 + - + -
88K CYS* 1.3 80.1 - - - +
90K GLN* 1.3 79.2 + - - +
91K TYR* 3.6 12.0 - - - +
96K LEU* 4.2 7.1 - - + +
97K THR 3.6 18.4 - - - +
98K PHE* 3.7 19.1 - - + -
104L TRP 3.1 24.5 + - - -
105L TYR* 4.1 0.6 - - - -
106L PHE* 3.3 16.9 - - - -
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Residues in contact with GLN 90 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2K ILE* 4.0 24.1 - - + +
4K MET* 3.5 24.0 - - + +
29K VAL* 3.8 22.2 - - + -
32K TYR 3.4 7.9 - - - +
33K LEU* 4.0 1.5 - - + +
89K GLN* 1.3 86.3 + - - +
91K TYR* 1.3 61.1 + - - +
92K ASP* 3.4 2.1 + - - +
93K LYS* 3.1 28.1 + - - +
95K PRO 3.0 24.4 + - - -
96K LEU* 4.1 6.2 - - - +
97K THR* 2.8 36.2 + - - +
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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