Contacts of the strand formed by residues 333 - 337 (chain R) in PDB entry 5A31
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 VAL 333 (chain R).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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326R SER 3.2 9.4 - - - +
332R VAL* 1.3 75.9 - - - +
334R HIS* 1.3 71.2 + - - +
346R THR* 3.2 6.1 - - - +
347R PHE* 2.7 67.2 + - + +
350R HIS* 4.2 10.3 - - + -
354R VAL* 3.6 36.8 - - + -
357R MET* 3.6 14.6 - - + -
367R LEU* 4.2 7.9 - - + -
369R THR* 4.1 14.8 - - + -
381R TRP* 5.3 0.2 - - - +
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Residues in contact with HIS 334 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
307R SER* 2.9 41.7 + - - -
308R HIS* 3.7 21.1 - + - -
325R ALA* 3.2 5.4 - - - +
326R SER* 2.8 42.2 + - - +
332R VAL* 3.5 11.7 - - + +
333R VAL* 1.3 74.2 - - - +
335R VAL* 1.3 64.5 + - - +
336R TYR* 3.5 14.1 - - + +
343R PRO* 3.5 19.8 - - + +
345R LEU 3.5 1.1 - - - -
346R THR* 3.0 43.6 + - + +
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Residues in contact with VAL 335 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
323R LYS* 4.7 4.9 - - + +
324R LEU 3.3 9.9 - - - +
325R ALA* 4.8 0.9 - - + -
333R VAL* 4.7 0.7 - - + -
334R HIS* 1.3 79.9 - - - +
336R TYR* 1.3 63.6 + - - +
343R PRO* 3.3 2.6 - - - +
344R ILE* 2.7 37.1 + - + +
345R LEU* 3.0 21.2 + - + +
347R PHE* 3.9 29.4 - - + -
359R TRP* 4.0 13.5 - - + -
367R LEU* 4.0 13.0 - - + -
383R VAL* 3.8 32.3 - - + -
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Residues in contact with TYR 336 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
290R ILE* 3.6 9.9 - - + +
305R ILE* 3.8 24.4 - - + +
307R SER* 2.8 22.7 + - - -
323R LYS* 3.4 9.1 - - - +
324R LEU* 2.8 60.4 + - + +
326R SER* 2.7 37.4 + - - -
334R HIS* 3.5 14.2 - - + +
335R VAL* 1.3 76.2 - - - +
337R GLU* 1.3 63.2 + - - +
338R GLY 3.5 14.5 + - - +
340R SER 3.8 19.7 - - - +
341R LYS 4.3 0.7 - - - -
342R SER 4.0 0.9 - - - +
343R PRO* 3.6 31.4 - - + -
344R ILE* 4.3 3.1 - - - +
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Residues in contact with GLU 337 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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322R ASN 3.9 4.7 - - - +
323R LYS* 4.3 22.8 + - + +
335R VAL 4.5 0.2 + - - -
336R TYR* 1.3 70.1 - - - +
338R GLY* 1.3 66.8 + - - +
339R THR 3.4 0.3 + - - -
340R SER* 3.0 28.4 + - - -
342R SER 5.1 0.8 + - - -
344R ILE* 4.1 37.4 - - + +
384R ASN* 6.2 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