Contacts of the strand formed by residues 139 - 143 (chain B) in PDB entry 6JKG
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 139 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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38B LYS* 6.1 3.4 - - - +
99B ASN* 3.3 14.2 + - - +
100B THR* 3.1 30.2 + - - +
101B VAL 2.8 32.1 + - - +
137B VAL* 3.5 6.4 - - - +
138B GLN* 1.3 92.8 - - + +
140B LEU* 1.3 54.1 + - - +
141B ILE* 4.1 7.9 - - + -
193B PHE* 4.6 0.2 - - - -
194B LEU* 3.3 12.3 - - + +
251B ALA* 3.8 24.2 + - - +
252B GLU* 4.9 2.4 - - - +
254B LEU* 4.1 18.6 - - + -
255B SER* 3.6 28.6 + - - +
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Residues in contact with LEU 140 (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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101B VAL* 3.3 36.1 - - + +
103B HIS* 4.3 14.4 - - + +
128B VAL* 4.1 22.2 - - + +
129B ILE* 4.2 20.6 - - + -
132B CYS* 4.1 11.2 - - - -
139B LYS* 1.3 73.2 - - - +
141B ILE* 1.3 64.7 + - - +
142B LEU* 5.5 0.7 - - + -
183B VAL* 4.4 21.7 - - + +
193B PHE* 4.1 23.9 - - + -
194B LEU 3.0 8.1 + - - -
195B THR* 3.3 8.8 - - + -
196B THR 2.9 26.7 + - - +
254B LEU* 5.8 0.4 - - - -
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Residues in contact with ILE 141 (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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100B THR* 3.6 29.8 - - + -
101B VAL 2.8 9.9 + - - -
102B PHE* 3.7 16.1 - - + -
103B HIS 3.1 24.6 + - - +
139B LYS* 4.0 10.8 - - + +
140B LEU* 1.3 75.3 - - - +
142B LEU* 1.3 63.9 + - - +
143B THR* 3.9 0.9 + - - +
196B THR* 3.3 27.1 - - + -
198B ILE* 4.2 6.3 - - + -
247B HIS* 4.0 30.7 - - + +
251B ALA* 3.7 31.0 - - + -
254B LEU* 5.0 3.1 - - + -
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Residues in contact with LEU 142 (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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103B HIS* 3.8 17.5 - - + +
140B LEU* 3.9 2.5 + - + +
141B ILE* 1.3 74.0 - - - +
143B THR* 1.3 72.5 + - - +
144B SER* 3.9 11.4 - - - -
179B GLN* 2.8 39.9 - - + +
180B GLU* 3.5 35.2 - - - +
183B VAL* 3.8 26.2 - - + -
196B THR 2.6 15.8 + - - +
197B ALA* 3.4 14.3 - - + -
198B ILE* 2.9 30.1 + - - +
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Residues in contact with THR 143 (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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49B LEU* 4.4 7.6 - - + -
53B MET* 3.9 0.7 - - + -
103B HIS 2.7 18.7 + - - +
104B CYS* 2.9 43.2 + - - +
105B ALA 5.6 0.5 - - - +
141B ILE 4.6 1.8 - - - +
142B LEU* 1.3 76.5 - - - +
144B SER* 1.3 63.0 + - - +
176B LYS* 3.0 16.6 + - - -
179B GLN* 5.0 0.5 + - - -
198B ILE 3.7 4.9 - - - -
200B PRO* 5.4 2.9 - - - -
247B HIS* 2.5 42.0 - - + +
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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