Contacts of the strand formed by residues 68 - 73 (chain J) 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 PHE 68 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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38J ARG* 4.6 2.0 - - - -
48J VAL* 5.2 1.3 - - + -
60J TYR* 2.5 32.3 + - + -
64J VAL* 3.1 48.9 + - + -
66J GLY 3.7 3.1 + - - -
67J ARG* 1.3 118.1 - - + +
69J THR* 1.3 57.3 + - - +
81J LEU* 4.0 17.7 - - + -
82J GLN 3.3 4.0 - - - +
83J MET* 3.3 51.1 - - + -
84J ASN 4.7 1.1 - - - -
86J LEU* 3.7 8.7 - - + -
90J ASP* 3.2 24.7 - - - -
94J TYR* 4.8 3.4 - + - -
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Residues in contact with THR 69 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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212F LYS* 5.7 8.5 - - - -
60J TYR* 3.6 4.5 - - - +
67J ARG 4.1 0.8 + - - -
68J PHE* 1.3 72.7 + - - +
70J ILE* 1.3 70.3 + - - +
71J SER* 4.1 8.9 + - - +
80J TYR 3.9 0.3 - - - +
81J LEU* 3.3 3.7 - - - -
82J GLN* 2.6 54.5 + - + +
84J ASN* 4.7 7.3 + - - -
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Residues in contact with ILE 70 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34J MET 4.5 2.7 - - - +
36J TRP* 3.7 21.8 - - + -
49J SER* 3.7 24.2 - - - +
50J TRP* 3.9 18.6 - - - +
51J ILE* 3.6 36.0 - - + +
58J THR* 4.0 17.2 - - + +
60J TYR* 3.1 26.0 + - + +
68J PHE 4.0 0.6 + - - -
69J THR* 1.3 80.1 - - - +
71J SER* 1.3 65.7 + - - +
79J LEU* 4.2 7.0 - - + -
80J TYR 3.3 15.3 - - - +
81J LEU* 4.3 2.8 - - + +
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Residues in contact with SER 71 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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207F LYS 5.9 0.4 - - - -
210F ASN* 3.3 32.8 + - - -
212F LYS* 5.6 2.0 - - - -
19J ARG* 5.5 0.7 + - - -
51J ILE* 3.7 9.4 - - - -
69J THR* 4.7 8.9 + - - +
70J ILE* 1.3 75.9 - - - +
72J ARG* 1.3 61.0 + - - +
79J LEU* 3.8 2.6 - - - +
80J TYR* 2.9 47.1 + - - +
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Residues in contact with ARG 72 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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207F LYS 3.1 28.5 + - - +
208F PRO 3.9 1.1 - - - +
209F SER 3.8 0.3 - - - -
210F ASN* 3.3 11.1 + - - +
29J PHE* 2.8 54.3 + - + -
30J SER* 4.3 3.0 - - - +
32J TYR 2.9 23.1 + - - -
34J MET* 3.9 5.2 - - - +
51J ILE* 3.5 34.7 + - + +
52J GLY 3.1 28.4 + - - -
53J PRO* 4.1 3.6 - - - -
54J SER* 3.8 3.8 - - - +
55J GLY* 3.6 15.5 - - - +
71J SER* 1.3 75.6 - - - +
73J ASP* 1.3 60.5 + - - +
74J ASN* 3.3 18.4 + - - +
78J THR 3.8 10.1 - - - +
79J LEU* 4.4 4.7 - - + -
80J TYR* 4.6 0.4 - - - -
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Residues in contact with ASP 73 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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209F SER* 3.3 28.7 - - - +
210F ASN* 4.2 3.1 + - + +
29J PHE* 4.4 0.2 - - - -
72J ARG* 1.3 74.0 - - - +
74J ASN* 1.3 60.9 + - - +
75J SER* 3.2 21.5 + - - -
76J LYS* 2.9 41.1 + - + +
77J ASN* 3.0 23.2 + - - -
78J THR* 3.2 15.1 + - - +
80J TYR* 3.8 22.7 + - + +
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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