Contacts of the strand formed by residues 102 - 106 (chain L) in PDB entry 2CK0
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 LYS 102 (chain L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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9L SER 3.0 15.7 + - - +
10L SER* 3.2 15.9 + - - +
11L LEU* 2.7 34.1 + - - +
84L ALA 3.6 10.3 - - - +
85L VAL* 4.0 19.5 - - + +
100L GLY 4.3 0.2 - - - -
101L THR* 1.3 73.4 - - - +
103L LEU* 1.3 61.5 + - - +
104L GLU* 4.6 18.3 + - + +
164L ASP* 5.8 4.7 - - - +
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Residues in contact with LEU 103 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11L LEU* 3.5 19.7 - - + -
13L VAL* 4.3 14.4 - - + -
19L VAL* 4.2 22.9 - - + -
21L MET* 5.0 4.0 - - + -
75L ILE* 4.7 7.6 - - + -
78L VAL* 3.9 23.1 - - + -
82L ASP* 3.6 27.6 - - + +
83L LEU* 3.6 21.1 - - - +
84L ALA 3.0 17.1 + - - +
86L TYR* 4.0 18.2 - - + +
101L THR 3.9 0.2 + - - -
102L LYS* 1.3 76.6 - - - +
104L GLU* 1.3 73.4 + - - +
105L ILE* 4.9 1.3 - - + -
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Residues in contact with GLU 104 (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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10L SER* 2.9 25.9 + - - +
11L LEU 2.7 14.7 + - - +
12L ALA* 3.1 16.4 - - + +
13L VAL 3.1 25.3 + - - +
102L LYS* 4.6 15.9 + - + +
103L LEU* 1.3 83.2 - - - +
105L ILE* 1.3 67.5 + - - +
139L TYR* 5.9 2.0 - - + +
141L LYS* 5.2 7.1 - - - +
165L GLN* 3.6 12.1 - - + +
172L TYR* 3.8 19.0 + - - +
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Residues in contact with ILE 105 (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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12L ALA* 5.5 0.2 - - - -
13L VAL* 3.4 10.1 - - + +
15L ALA* 4.4 17.9 - - + +
78L VAL* 3.8 30.7 - - + +
79L GLN 3.8 13.5 - - - +
80L ALA* 4.2 11.0 - - + -
83L LEU* 3.8 24.9 - - + -
103L LEU* 4.9 6.1 - - + -
104L GLU* 1.3 75.8 - - - +
106L LYS* 1.3 72.6 + - - +
107L ARG* 3.3 6.2 + - + +
139L TYR* 3.6 7.2 - - - -
165L GLN* 2.8 37.6 + - - +
170L SER* 4.1 15.9 - - - +
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Residues in contact with LYS 106 (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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12L ALA* 3.7 31.6 + - + +
13L VAL 2.8 14.5 + - - +
14L SER* 3.3 37.5 + - - +
15L ALA 4.5 1.0 + - - -
17L GLU* 4.4 11.5 + - - -
104L GLU 3.7 1.8 + - - -
105L ILE* 1.3 73.3 - - - +
107L ARG* 1.3 60.4 + - - +
139L TYR* 3.5 16.8 - - + +
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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