Contacts of the strand formed by residues 18 - 25 (chain G) in PDB entry 5DK3
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 VAL 18 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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10G GLU* 3.6 43.3 - - + +
12G LYS* 4.0 10.5 - - + +
17G SER* 1.3 75.7 - - - +
19G LYS* 1.3 62.8 + - - +
20G VAL* 4.5 13.7 - - + -
81G MET* 3.7 2.8 - - + +
82G GLU* 3.2 5.6 - - - +
83G LEU* 2.8 53.3 + - + +
86G LEU* 3.9 22.4 - - + -
94G TYR* 6.1 0.9 - - + -
116G VAL* 4.5 14.1 - - + -
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Residues in contact with LYS 19 (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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7G SER* 4.6 1.9 + - - -
10G GLU* 4.0 13.9 - - - +
18G VAL* 1.3 74.6 - - - +
20G VAL* 1.3 62.4 + - - +
21G SER 4.2 0.5 + - - -
71G THR* 4.4 10.4 + - - +
80G TYR* 3.7 43.7 - - + -
81G MET 3.4 4.0 - - - +
82G GLU* 4.1 30.2 + - + -
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Residues in contact with VAL 20 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6G GLN* 3.8 10.3 - - - +
7G SER* 3.7 8.3 - - - +
10G GLU* 5.1 1.6 - - + -
18G VAL* 4.5 14.6 - - + -
19G LYS* 1.3 76.3 - - - +
21G SER* 1.3 67.7 + - - +
36G TRP* 3.9 10.8 - - + -
80G TYR* 3.2 6.8 - - - +
81G MET* 2.9 56.4 + - + +
94G TYR* 4.8 4.3 - - + -
114G THR* 3.4 41.7 - - + +
116G VAL* 4.5 8.3 - - + -
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Residues in contact with SER 21 (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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5G VAL 5.4 0.3 + - - -
6G GLN* 3.3 7.8 - - - +
7G SER* 2.9 47.5 + - - -
19G LYS 4.2 1.0 + - - -
20G VAL* 1.3 76.1 - - - +
22G CYS* 1.3 60.4 + - - +
23G LYS 4.1 1.5 + - - -
36G TRP* 4.4 1.3 - - - -
78G THR* 4.0 7.4 - - - -
79G ALA 3.4 5.6 - - - -
80G TYR* 3.7 26.5 - - - -
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Residues in contact with CYS 22 (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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4G LEU* 4.0 17.9 - - - -
5G VAL 3.5 5.2 - - - -
6G GLN* 4.5 0.7 - - - -
21G SER* 1.3 74.4 - - - +
23G LYS* 1.3 62.5 + - - +
24G ALA* 3.5 2.6 + - - +
34G MET* 4.1 15.6 - - - +
36G TRP* 3.7 7.2 - - + -
77G THR 4.0 0.2 - - - +
78G THR* 3.4 2.9 - - - -
79G ALA* 2.8 38.0 + - + +
96G CYS* 2.0 54.5 - - + -
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Residues in contact with LYS 23 (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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3G GLN 3.7 1.4 - - - +
4G LEU* 3.4 2.7 - - - -
5G VAL* 2.7 51.3 + - + +
21G SER* 4.1 1.2 + - - -
22G CYS* 1.3 69.6 - - - +
24G ALA* 1.3 65.1 + - - +
25G SER* 5.2 4.5 + - - -
76G THR* 2.7 41.2 + - - +
77G THR* 3.8 6.9 + - - -
78G THR* 3.7 14.4 + - + +
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Residues in contact with ALA 24 (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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3G GLN 3.4 5.4 - - - -
4G LEU* 3.8 9.4 - - + -
22G CYS 3.5 1.6 + - - -
23G LYS* 1.3 78.7 - - - +
25G SER* 1.3 65.0 + - - +
27G TYR* 3.5 28.0 - - + +
29G PHE* 3.5 20.6 - - + -
34G MET* 4.4 2.2 - - + -
77G THR* 2.8 38.6 + - - +
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Residues in contact with SER 25 (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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1G GLN 4.1 1.5 + - - -
3G GLN* 2.9 58.2 + - - +
5G VAL* 5.9 0.5 - - - +
23G LYS* 5.2 5.8 + - - -
24G ALA* 1.3 77.1 - - - +
26G GLY* 1.3 62.7 + - - +
27G TYR* 3.4 11.3 - - - +
77G THR* 5.0 0.9 - - - -
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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