Contacts of the strand formed by residues 102 - 106 (chain G) 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 THR 102 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6G GLN* 3.5 15.0 + - - +
7G SER 4.3 4.4 + - - +
8G PRO* 3.1 27.1 + - + +
9G GLY 3.5 6.3 - - - +
10G THR 4.6 0.2 - - - -
11G LEU* 4.2 17.0 - - + -
21G LEU* 3.8 28.7 - - + +
22G SER 4.8 1.9 + - - -
84G ALA 3.5 1.2 - - - +
85G VAL* 3.3 4.8 - - - -
86G TYR* 2.8 34.2 + - - -
101G GLY* 1.3 77.5 + - - -
103G LYS* 1.3 75.9 + - - +
104G VAL* 4.8 0.2 - - + -
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Residues in contact with LYS 103 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9G GLY 3.0 11.7 + - - +
10G THR* 3.6 13.2 - - + +
11G LEU* 3.2 23.2 + - - +
84G ALA* 3.5 4.7 - - - +
85G VAL* 4.1 25.9 - - + +
101G GLY 4.2 0.4 - - - -
102G THR* 1.3 79.3 - - - +
104G VAL* 1.3 67.2 + - - +
105G GLU* 4.1 15.8 - - + +
142G ARG* 5.1 10.8 - - - +
165G GLU* 3.8 24.3 + - - +
166G GLN* 5.6 2.6 - - - +
173G TYR* 5.6 4.6 + - - -
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Residues in contact with VAL 104 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11G LEU* 3.5 25.4 - - + +
13G LEU* 4.8 10.3 - - + -
19G ALA* 5.3 1.8 - - + -
21G LEU* 4.4 12.8 - - + -
75G ILE* 5.6 1.1 - - + -
78G LEU* 4.8 15.0 - - + -
82G ASP 4.3 4.0 - - - +
83G PHE* 3.3 43.1 - - + +
84G ALA 2.9 18.8 + - - +
86G TYR* 3.9 25.4 - - + -
102G THR* 4.5 0.4 - - + +
103G LYS* 1.3 80.8 + - - +
105G GLU* 1.3 60.4 + - - +
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Residues in contact with GLU 105 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10G THR* 4.8 13.9 - - + +
11G LEU 2.9 13.3 + - - +
12G SER* 3.0 16.8 + - - -
13G LEU* 3.0 26.5 + - - +
83G PHE* 3.5 9.7 - - - -
103G LYS* 4.1 14.6 - - + +
104G VAL* 1.3 72.6 - - - +
106G ILE* 1.3 66.6 + - - +
140G TYR* 2.9 29.4 + - - -
142G ARG* 5.8 1.2 + - - +
166G GLN* 2.9 27.6 - - - +
173G TYR* 3.1 20.4 + - - +
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Residues in contact with ILE 106 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12G SER* 4.6 0.2 - - - -
13G LEU 3.5 2.2 - - - -
15G PRO* 3.8 21.3 - - + -
80G SER* 5.1 2.7 - - - +
83G PHE* 3.4 44.2 - - + -
105G GLU* 1.3 83.1 - - - +
107G LYS* 1.3 73.8 + - - +
108G ARG* 4.4 0.7 - - - +
140G TYR* 3.3 5.4 + - - -
166G GLN* 2.9 42.1 - - + +
171G SER* 3.5 23.6 - - - +
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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