Contacts of the strand formed by residues 343 - 348 (chain A) in PDB entry 1OOA
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 343 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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250A ILE* 3.6 48.5 + - + +
251A VAL 3.9 14.5 + - - -
252A ARG* 4.9 3.2 - - - +
253A MET* 5.3 7.6 - - - -
328A PHE* 3.2 5.8 - - - -
329A VAL* 2.8 40.5 + - + +
341A GLU 4.2 7.9 - - - +
342A PRO* 1.3 79.1 - - - +
344A PRO* 1.3 76.5 - - + +
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Residues in contact with PRO 344 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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253A MET* 5.8 1.9 - - - +
256A THR* 4.2 18.5 - - - +
326A SER* 4.7 9.2 - - - +
327A VAL 3.5 9.9 - - - +
328A PHE* 4.1 14.6 - - + -
329A VAL* 4.7 1.2 - - - +
342A PRO 4.6 1.8 - - - +
343A LYS* 1.3 94.4 - - + +
345A PHE* 1.3 60.4 + - - +
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Residues in contact with PHE 345 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
253A MET* 4.5 4.7 - - + -
255A ARG 4.4 1.1 - - - -
256A THR* 3.3 20.0 - - - -
257A ALA 3.5 31.0 - - - -
258A GLY* 3.6 4.9 - - - -
266A ILE* 3.7 22.0 - - + -
282A PHE* 3.8 15.0 - + - -
313A THR* 3.9 19.5 - - + -
326A SER* 3.6 3.9 + - - -
327A VAL* 2.8 50.8 + - + +
329A VAL* 3.2 32.3 - - + -
343A LYS 3.7 0.2 + - - -
344A PRO* 1.3 72.0 - - - +
346A LEU* 1.3 69.5 + - - +
347A TYR* 4.1 24.0 - + - -
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Residues in contact with LEU 346 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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256A THR 2.9 10.9 + - - +
257A ALA* 3.0 23.0 - - + +
258A GLY 2.8 32.1 + - - +
324A PRO* 3.7 31.4 - - + -
325A ALA 3.8 15.9 - - - +
326A SER* 4.2 10.1 - - - +
345A PHE* 1.3 77.1 - - - +
347A TYR* 1.3 58.0 + - - +
348A TYR* 3.9 7.9 + - + -
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Residues in contact with TYR 347 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
258A GLY 3.2 4.7 - - - -
259A CYS 3.7 16.2 - - - -
260A VAL* 3.6 28.5 - - + -
282A PHE* 4.2 4.1 - + - -
292A TRP* 3.9 10.0 - + - -
313A THR* 4.5 3.6 - - - -
314A PRO* 2.7 48.6 + - - +
316A TYR* 3.4 40.4 - + + -
321A ILE* 4.3 1.0 - - - +
324A PRO* 3.2 4.3 - - - +
325A ALA* 2.8 41.8 + - + +
327A VAL* 3.7 30.1 - - + -
345A PHE* 4.1 19.1 - + - -
346A LEU* 1.3 73.6 - - - +
348A TYR* 1.3 59.2 + - - +
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Residues in contact with TYR 348 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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257A ALA* 3.9 15.2 + - + -
258A GLY* 2.8 40.7 + - - -
259A CYS* 3.4 18.2 + - + -
260A VAL* 3.0 27.1 + - - -
264A GLU* 4.3 6.6 + - - -
321A ILE* 4.8 0.2 - - - -
324A PRO* 4.3 9.2 - - + -
346A LEU* 4.1 10.3 - - + -
347A TYR* 1.3 74.8 - - - +
349A PRO* 1.3 86.1 - - + +
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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