Contacts of the helix formed by residues 57 - 65 (chain B) in PDB entry 5JKC
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 57 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32B HIS 5.6 2.6 + - - +
34B LYS* 4.0 23.2 - - + +
40B GLU* 4.1 8.3 - - - +
43B LEU* 3.9 2.7 - - - -
56B CYS* 1.3 75.5 - - - +
58B LEU* 1.3 66.1 + - - +
59B THR* 3.6 11.0 + - - -
60B THR* 3.0 27.5 + - - +
61B SER* 3.0 21.8 + - - -
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Residues in contact with LEU 58 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163A TYR* 3.6 45.3 - - + +
40B GLU* 4.2 8.0 + - - +
42B LYS* 3.2 44.2 - - + +
43B LEU* 4.0 10.3 - - - +
44B TYR* 4.4 4.7 - - + +
57B THR* 1.3 73.5 - - - +
59B THR* 1.3 68.0 + - - +
61B SER* 2.6 23.9 + - - +
62B TRP* 2.9 9.8 + - + +
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Residues in contact with THR 59 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57B THR* 3.2 9.8 + - - -
58B LEU* 1.3 83.0 - - - +
60B THR* 1.3 58.1 + - - +
62B TRP* 3.2 11.3 + - + +
63B GLU* 2.8 56.4 + - + +
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Residues in contact with THR 60 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32B HIS* 4.0 18.0 + - + +
56B CYS* 3.9 18.4 - - + -
57B THR* 3.0 27.7 + - - -
59B THR* 1.3 75.4 - - - +
61B SER* 1.3 66.2 + - - +
63B GLU* 3.1 12.1 + - - +
64B ALA* 3.0 23.3 + - + +
71B LEU* 4.1 10.7 - - + +
98B GLU* 3.9 32.1 - - + +
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Residues in contact with SER 61 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43B LEU* 3.7 8.2 - - - -
44B TYR* 3.0 23.7 + - - +
47B CYS* 3.7 35.7 - - - -
56B CYS* 4.7 2.7 - - - +
57B THR 3.0 11.6 + - - -
58B LEU* 2.6 23.8 + - - -
60B THR* 1.3 77.8 - - - +
62B TRP* 1.3 53.3 + - - +
64B ALA* 3.5 3.7 + - - +
65B HIS* 2.6 35.9 + - - -
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Residues in contact with TRP 62 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141A VAL* 4.1 9.0 - - + -
160A ARG* 3.7 22.0 - - + -
161A LYS 3.0 31.9 - - - -
162A SER* 3.7 3.6 - - - +
163A TYR* 3.2 50.6 - + + +
44B TYR* 3.8 50.9 - + + -
58B LEU* 2.9 9.6 + - + +
59B THR* 3.6 15.0 - - + +
61B SER* 1.3 82.8 + - - +
63B GLU* 1.3 74.3 + - + +
65B HIS* 3.0 19.1 + - - +
66B LEU* 3.5 34.3 + - + +
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Residues in contact with GLU 63 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32B HIS* 5.4 1.2 + - - -
59B THR* 2.8 41.4 + - + +
60B THR* 3.1 8.7 + - - +
62B TRP* 1.3 86.5 - - + +
64B ALA* 1.3 53.7 + - - +
66B LEU* 3.2 14.9 + - + +
69B SER* 1.6 37.9 + - - +
70B PRO* 3.8 23.4 - - + +
71B LEU* 3.4 26.5 - - + +
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Residues in contact with ALA 64 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47B CYS* 4.6 7.9 - - - -
60B THR* 3.0 10.9 + - + +
61B SER* 3.5 15.0 - - - +
62B TRP 3.1 0.2 + - - -
63B GLU* 1.3 78.4 - - - +
65B HIS* 1.3 65.6 + - + +
66B LEU 3.6 4.3 + - - +
69B SER* 3.6 4.6 + - - -
71B LEU* 3.9 7.8 - - + +
91B ILE* 3.9 12.7 - - + +
94B ILE* 3.4 46.1 - - + +
95B CYS* 4.7 0.2 - - - -
98B GLU* 5.8 1.3 - - + -
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Residues in contact with HIS 65 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
160A ARG* 3.2 34.5 + - - +
44B TYR* 3.4 37.3 - + + -
45B GLU* 3.3 9.8 - - + +
46B GLU* 3.3 26.1 + - + -
61B SER 2.6 30.1 + - - -
62B TRP 3.0 7.2 + - - +
64B ALA* 1.3 79.7 - - + +
66B LEU* 1.3 57.8 + - - +
87B ARG* 2.9 27.3 + - - -
91B ILE* 3.6 35.1 - - + +
95B CYS* 4.1 10.1 - - - -
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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