Contacts of the strand formed by residues 101 - 105 (chain F) in PDB entry 4KJQ
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 101 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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6F GLN* 3.2 29.0 + - - +
7F SER 4.8 0.2 + - - -
8F PRO* 3.1 28.4 + - + +
9F ALA 3.4 4.5 - - - +
11F MET* 4.2 20.6 - - + -
21F MET* 4.0 33.9 - - + +
22F THR 5.0 0.2 + - - -
83F ALA 3.6 1.0 - - - +
84F THR* 3.5 2.0 - - - +
85F TYR* 3.0 31.1 + - - -
100F GLY* 1.3 69.0 - - - -
102F LYS* 1.3 63.8 + - - +
103F LEU 3.5 2.4 + - - -
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Residues in contact with LYS 102 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9F ALA 3.0 14.4 + - - +
10F ILE* 3.3 19.0 - - + +
11F MET 2.9 27.0 + - - +
39F SER* 5.0 1.8 + - - -
83F ALA 3.7 6.9 - - - +
84F THR* 3.9 22.5 + - + +
101F THR* 1.3 70.2 - - - +
103F LEU* 1.3 64.7 + - - +
104F GLU* 3.4 32.5 - - + +
164F ASP* 3.4 29.5 + - - +
165F GLN* 5.6 3.0 - - - +
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Residues in contact with LEU 103 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11F MET* 3.7 25.1 - - + +
13F ALA* 4.5 5.6 - - + -
19F VAL* 4.1 14.6 - - + -
21F MET* 3.8 20.4 - - + -
74F ILE* 3.7 28.0 - - + -
77F MET* 3.3 32.1 - - + -
81F ASP 4.0 8.7 - - - +
82F ALA* 3.7 20.4 - - - +
83F ALA* 2.9 19.1 + - - +
85F TYR* 4.3 2.9 - - + -
101F THR 3.5 0.4 + - - -
102F LYS* 1.3 76.5 - - - +
104F GLU* 1.3 68.5 + - - +
165F GLN* 4.6 0.2 - - - +
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Residues in contact with GLU 104 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10F ILE* 3.8 23.3 - - + +
11F MET 2.7 20.1 + - - +
12F SER* 3.5 12.4 + - - +
13F ALA* 3.2 24.9 + - - +
77F MET* 4.4 0.2 - - - +
102F LYS* 3.4 31.1 - - + -
103F LEU* 1.3 81.1 - - - +
105F ILE* 1.3 67.4 + - - +
141F LYS* 5.3 9.8 - - - +
165F GLN* 3.5 11.2 + - - +
172F TYR* 3.6 19.6 + - - +
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Residues in contact with ILE 105 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13F ALA 3.6 1.3 - - - +
15F PRO* 3.6 31.4 - - + -
77F MET* 3.2 30.1 - - + -
79F ALA* 3.4 24.9 - - + +
82F ALA* 3.5 22.0 - - + -
104F GLU* 1.3 77.3 - - - +
106F LEU* 1.3 68.3 + - - +
107F ARG* 4.0 1.8 - - + -
139F TYR* 3.3 10.4 + - - -
165F GLN* 2.8 43.5 + - + +
166F ASP 5.4 0.4 - - - +
170F SER* 3.7 21.3 - - - +
172F TYR* 5.2 0.2 + - - -
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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