Contacts of the strand formed by residues 99 - 106 (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 GLY 99 (chain O).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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4O MET* 3.5 23.8 - - - -
6O GLN* 2.9 15.5 - - - +
87O TYR* 3.4 15.5 - - - +
88O CYS* 2.8 16.6 + - - -
98O PHE* 1.3 78.4 - - - +
100O GLY* 1.3 52.7 + - - -
101O GLY 2.7 19.1 + - - -
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Residues in contact with GLY 100 (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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4O MET 4.5 5.5 + - - -
5O THR* 6.3 0.2 - - - -
6O GLN* 5.4 4.8 - - - +
87O TYR* 3.5 13.0 - - - -
98O PHE 4.3 1.0 + - - -
99O GLY* 1.3 65.1 - - - -
101O GLY* 1.3 59.2 + - - -
44P GLY* 4.6 9.0 + - - -
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Residues in contact with GLY 101 (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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6O GLN* 2.9 22.8 + - - +
8O PRO 4.5 2.4 - - - +
9O GLY* 4.2 9.9 - - - +
85O VAL* 4.4 3.6 - - - -
86O TYR 3.4 6.5 - - - -
87O TYR* 3.4 15.9 - - - -
99O GLY 2.7 7.9 + - - -
100O GLY* 1.3 73.4 - - - -
102O THR* 1.3 66.3 + - - -
103O LYS 4.3 0.2 - - - -
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Residues in contact with THR 102 (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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6O GLN* 3.4 22.2 + - - +
7O SER 4.8 2.5 + - - -
8O PRO* 3.3 23.5 + - + +
9O GLY 3.8 3.8 - - - +
11O LEU* 4.5 15.9 - - + -
21O LEU* 3.5 33.9 - - + +
22O SER 5.3 1.0 + - - -
84O ALA 3.7 0.2 - - - +
85O VAL* 3.3 7.8 - - - +
86O TYR* 2.9 33.9 + - - -
101O GLY* 1.3 77.2 + - - -
103O LYS* 1.3 67.2 + - - +
104O VAL* 3.5 3.5 + - + -
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Residues in contact with LYS 103 (chain O).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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9O GLY 3.1 14.2 + - - +
10O THR* 3.5 18.4 - - + +
11O LEU 3.2 23.3 + - - -
84O ALA 3.7 4.7 - - - +
85O VAL* 3.8 24.3 - - + +
101O GLY 4.3 0.2 - - - -
102O THR* 1.3 70.0 - - - +
104O VAL* 1.3 70.9 + - - +
105O GLU* 3.4 10.6 + - + +
142O ARG* 4.7 13.7 - - - +
165O GLU* 4.3 21.2 + - - -
166O GLN* 5.0 3.2 - - - +
173O TYR* 4.0 30.3 + - - -
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Residues in contact with VAL 104 (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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11O LEU* 4.0 15.5 - - + +
13O LEU* 5.2 7.9 - - + -
19O ALA* 5.6 1.6 - - + -
21O LEU* 3.9 22.9 - - + -
75O ILE* 5.9 1.3 - - + -
78O LEU* 3.7 20.0 - - + -
82O ASP 4.1 5.6 - - - +
83O PHE* 3.5 38.2 - - + +
84O ALA 2.9 16.0 + - - +
86O TYR* 3.6 30.1 - - + -
102O THR* 4.4 5.6 - - + +
103O LYS* 1.3 74.1 - - - +
105O GLU* 1.3 60.9 + - - +
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Residues in contact with GLU 105 (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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10O THR* 3.4 31.4 - - + +
11O LEU 3.3 6.6 + - - +
12O SER* 3.0 19.3 + - - -
13O LEU 2.9 25.3 + - - +
83O PHE* 3.8 5.9 - - - -
103O LYS* 3.4 14.3 + - + +
104O VAL* 1.3 76.0 - - - +
106O ILE* 1.3 83.2 + - - +
140O TYR* 2.8 20.7 + - - -
141O PRO* 6.0 0.7 - - - +
142O ARG* 5.5 2.6 + - - +
166O GLN* 2.7 27.4 - - - +
173O TYR* 2.9 22.1 + - - +
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Residues in contact with ILE 106 (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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13O LEU 3.5 4.3 - - - -
15O PRO* 4.1 23.6 - - + -
80O SER 5.7 0.2 - - - +
83O PHE* 3.3 41.7 - - + -
105O GLU* 1.3 91.7 - - - +
107O LYS* 1.3 71.6 + - - +
108O ARG* 4.5 2.0 - - + +
140O TYR* 3.4 3.5 + - - -
166O GLN* 3.0 24.9 - - + +
167O ASP 6.1 0.2 - - - +
171O SER* 3.6 26.5 - - - +
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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