Contacts of the strand formed by residues 343 - 346 (chain B) in PDB entry 5K7W
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 ARG 343 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160B ILE* 4.3 16.4 - - - +
163B SER* 5.2 0.8 + - - -
164B ASN* 3.1 27.0 + - - +
186B PHE* 4.1 2.2 - - - -
188B VAL* 3.5 19.9 - - + +
334B ILE* 5.2 0.9 - - - +
335B GLU* 4.0 21.5 + - - +
338B CYS 4.9 4.9 + - - -
340B GLY 3.5 18.9 + - - +
341B ARG* 3.5 16.8 + - - +
342B ARG* 1.3 75.7 - - - +
344B LEU* 1.3 60.2 + - - +
356B GLY* 2.9 33.5 + - - +
357B TRP* 3.5 37.8 - - + +
358B LEU* 2.9 26.7 + - - +
374B TYR* 3.6 8.2 + - - -
386B THR* 4.2 20.2 - - - +
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Residues in contact with LEU 344 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
182B LEU* 4.2 6.3 - - + -
186B PHE* 3.6 26.7 - - + -
188B VAL 3.0 10.0 + - - +
189B ILE* 3.3 9.0 - - + +
190B LEU 2.8 31.2 + - - +
224B ILE* 3.5 33.0 - - + -
343B ARG* 1.3 73.6 - - - +
345B HIS* 1.3 58.3 + - - +
346B LEU* 3.7 24.0 - - + -
357B TRP* 3.5 4.9 - - - -
358B LEU* 3.4 26.9 - - + +
360B VAL* 3.7 29.2 - - + -
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Residues in contact with HIS 345 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
190B LEU* 3.4 30.4 - - + +
192B GLU* 2.9 31.4 + - + +
331B PHE* 3.6 26.3 - + + -
344B LEU* 1.3 73.4 - - - +
346B LEU* 1.3 65.9 + - - +
348B GLY* 3.6 15.1 + - - -
352B THR* 3.6 30.8 + - + -
357B TRP* 3.8 17.0 - - + -
358B LEU 2.8 13.6 + - - +
359B THR* 3.5 10.4 + - - +
360B VAL 3.0 27.9 + - - +
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Residues in contact with LEU 346 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174B ILE* 4.0 24.0 - - + -
177B PHE* 6.4 0.7 - - + -
179B ILE* 4.5 9.6 - - + -
182B LEU* 4.4 7.4 - - + -
189B ILE* 4.1 10.3 - - + -
190B LEU 2.8 11.5 + - - +
191B LEU* 4.0 18.6 - - + -
192B GLU 3.1 19.2 + - - -
219B LEU* 5.5 2.9 - - + -
221B ILE* 3.7 29.4 - - + -
344B LEU* 3.7 31.4 - - + -
345B HIS* 1.3 73.8 - - - +
347B PHE* 1.3 73.6 + - + +
348B GLY 3.6 0.3 + - - -
360B VAL* 3.4 21.1 - - + -
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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