Contacts of the strand formed by residues 304 - 308 (chain B) in PDB entry 5A86
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 LEU 304 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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166B PHE* 5.9 1.1 - - + -
169B PHE* 3.5 39.7 - - + +
172B PHE* 3.9 12.3 - - + -
213B LEU* 4.3 13.0 - - + -
214B GLN 3.3 7.0 - - - +
215B LEU* 3.5 37.7 - - + -
242B HIS* 4.4 7.9 - - + -
246B MET* 4.5 2.5 - - + -
301B CYS* 2.8 42.7 + - + +
302B GLY 3.8 1.7 - - - +
303B ARG* 1.3 81.2 - - + +
305B SER* 1.3 59.8 + - - +
306B TYR* 3.6 25.4 - - + +
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Residues in contact with SER 305 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
212B SER 3.8 0.3 - - - +
213B LEU* 3.5 5.2 - - - +
214B GLN* 2.9 43.2 + - - +
216B ARG* 3.0 37.4 + - - -
298B THR* 3.8 17.7 - - - +
299B TRP 3.4 5.8 - - - -
300B GLU* 4.3 8.5 - - - +
304B LEU* 1.3 71.7 + - - +
306B TYR* 1.3 65.3 + - - +
307B CYS* 4.0 1.3 + - - -
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Residues in contact with TYR 306 (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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211B VAL* 4.3 12.8 - - + -
212B SER 3.4 7.9 - - - +
213B LEU* 4.0 14.4 - - + -
242B HIS* 2.7 34.5 + + - -
246B MET* 3.4 33.9 - - + +
298B THR* 3.1 4.1 - - - -
299B TRP* 2.9 51.3 + - + +
301B CYS* 3.9 9.4 - - - -
304B LEU* 3.6 20.8 - - + +
305B SER* 1.3 75.4 - - - +
307B CYS* 1.3 60.2 + - - +
1432B D7E 2.9 61.0 - - + -
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Residues in contact with CYS 307 (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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211B VAL* 3.1 4.4 - - - -
212B SER* 2.8 49.2 + - - +
296B THR 3.8 11.7 - - - -
297B GLY 3.7 2.2 - - - -
298B THR* 3.4 23.1 - - + +
305B SER* 4.0 1.7 - - - -
306B TYR* 1.3 72.7 - - - +
308B LEU* 1.3 79.0 + - - +
309B GLU* 4.5 0.3 - - - -
310B ASP* 5.0 7.0 - - - -
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Residues in contact with LEU 308 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
208B SER* 4.9 7.0 - - - +
209B LEU 4.7 4.0 - - - +
210B LYS 3.9 7.9 - - - +
211B VAL* 3.9 18.8 - - + +
292B PHE* 4.2 6.7 - - + -
297B GLY* 3.0 35.1 + - - +
299B TRP* 3.7 23.6 - - + -
306B TYR 4.1 0.6 + - - -
307B CYS* 1.3 85.8 - - - +
309B GLU* 1.3 65.7 + - - +
310B ASP* 3.4 7.6 + - - +
318B LEU* 4.7 13.7 - - + -
324B LEU* 3.7 40.2 - - + -
328B TYR* 4.2 5.8 - - - +
1432B D7E 5.9 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