Contacts of the strand formed by residues 301 - 305 (chain A) in PDB entry 5C16
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 301 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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246A TRP* 3.7 37.2 - - + +
291A LEU* 3.9 4.5 - - + -
293A TRP* 3.3 8.5 - - - +
294A ILE* 3.6 20.2 - - + +
299A GLN 3.4 17.0 - - - +
300A ALA* 1.3 75.2 - - - +
302A ILE* 1.3 61.0 + - - +
303A THR* 4.0 9.9 + - - +
327A ILE* 4.4 2.9 + - - +
330A ALA* 6.1 0.2 - - + -
427A ILE* 3.2 10.0 - - - +
433A SER* 3.1 17.8 + - - +
434A VAL 2.8 29.8 + - - +
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Residues in contact with ILE 302 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
291A LEU* 3.7 0.5 - - - -
292A SER* 2.7 38.6 + - - -
293A TRP* 3.0 22.5 + - + +
301A THR* 1.3 74.1 - - - +
303A THR* 1.3 62.8 + - - +
423A ILE* 4.0 18.2 - - + -
427A ILE* 3.7 17.5 - - + -
434A VAL* 3.5 5.4 - - + -
436A VAL* 4.1 11.9 - - + -
449A THR* 4.0 25.6 - - + +
452A ALA* 4.3 7.9 - - + -
453A MET* 4.3 15.5 - - + -
456A LEU* 3.9 27.1 - - + -
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Residues in contact with THR 303 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
246A TRP* 3.6 31.4 - - + -
289A PRO* 4.3 6.8 - - - +
290A VAL* 3.1 21.8 - - - +
291A LEU* 3.8 8.7 - - + -
292A SER 4.9 0.2 - - - -
301A THR* 4.0 9.0 - - - +
302A ILE* 1.3 81.8 - - - +
304A ARG* 1.3 62.7 + - - +
327A ILE* 4.2 12.3 - - + +
434A VAL 3.0 6.1 + - - +
435A VAL* 3.2 30.6 - - - +
436A VAL 3.0 22.1 + - - -
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Residues in contact with ARG 304 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
261A TYR* 3.6 3.5 + - - +
287A ARG* 3.6 11.3 - - - +
288A VAL 3.2 2.9 - - - +
289A PRO* 3.1 3.8 - - - +
290A VAL* 3.0 41.0 + - + +
292A SER* 3.4 19.3 - - - +
303A THR* 1.3 75.6 - - - +
305A CYS* 1.3 64.4 + - - +
436A VAL 3.4 6.3 - - - +
441A GLY 3.1 23.8 + - - -
442A TRP* 4.0 3.8 - - - +
445A THR* 3.8 23.8 - - + +
446A ALA* 3.9 19.3 - - - +
449A THR* 3.9 16.5 + - + -
473A GLU* 2.8 41.0 + - - -
477A PHE* 3.7 32.0 + - - +
479A HIS 5.9 0.6 - - - +
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Residues in contact with CYS 305 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
261A TYR* 3.9 5.6 - - - -
283A ARG* 3.6 13.9 - - - +
287A ARG* 3.3 18.2 - - - +
289A PRO* 3.5 20.0 - - + -
304A ARG* 1.3 77.9 - - - +
306A SER* 1.3 67.0 + - - +
435A VAL* 3.6 24.7 - - - -
436A VAL 3.1 7.1 + - - +
437A HIS* 3.1 36.6 - - - +
441A GLY* 3.4 17.1 - - - -
445A THR* 3.8 1.9 + - - +
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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
------------------------------------------------------------
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