Contacts of the strand formed by residues 330 - 336 (chain O) in PDB entry 5GJQ
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 330 (chain O).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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290O GLN* 4.2 18.6 - - + -
291O LEU 3.0 11.4 - - - +
292O THR* 5.0 2.2 - - - -
293O PHE* 3.6 3.5 - - - -
324O ILE* 3.8 0.3 - - - -
325O ASP* 2.9 41.0 + - + +
328O ASP* 4.0 15.7 - - + +
329O LYS* 1.3 77.0 - - - +
331O VAL* 1.3 69.5 + - - +
332O HIS 4.3 0.9 - - - +
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Residues in contact with VAL 331 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277O LEU* 6.1 1.6 - - + -
290O GLN* 3.0 10.1 - - - -
291O LEU* 2.8 37.8 + - + +
293O PHE* 3.6 23.8 - - + -
296O ILE* 4.1 15.7 - - + -
311O VAL* 4.2 28.0 - - + -
323O SER 3.7 12.8 - - - +
324O ILE* 4.7 6.3 - - + -
330O ARG* 1.3 81.9 - - - +
332O HIS* 1.3 63.3 + - - +
333O MET* 3.7 22.9 + - + +
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Residues in contact with HIS 332 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
289O ARG 4.1 9.6 - - - +
290O GLN* 4.6 5.6 - - + +
322O GLY* 3.5 4.2 - - - -
323O SER* 2.9 52.2 + - - +
324O ILE* 5.3 0.2 - - - +
325O ASP 5.7 0.2 - - - +
330O ARG* 4.3 1.0 - - - +
331O VAL* 1.3 74.3 - - - +
333O MET* 1.3 58.4 + - - +
334O THR* 4.4 3.6 - - - -
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Residues in contact with MET 333 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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277O LEU* 6.1 2.5 - - + -
281O THR* 3.8 28.5 - - - +
289O ARG* 3.9 30.2 + - + +
290O GLN 5.5 0.4 - - - +
291O LEU* 5.3 6.7 - - + -
320O VAL* 5.6 8.5 - - + -
321O LYS 3.3 10.5 - - - +
322O GLY* 4.1 0.7 - - - -
331O VAL* 3.7 26.2 + - + +
332O HIS* 1.3 75.5 - - - +
334O THR* 1.3 67.7 + - - +
335O TRP* 3.5 0.4 - - - -
336O VAL* 4.9 9.2 - - + -
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Residues in contact with THR 334 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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289O ARG* 4.0 9.0 + - - -
321O LYS* 2.8 23.2 + - - +
322O GLY* 3.4 9.9 - - - -
332O HIS* 3.7 4.3 - - - -
333O MET* 1.3 73.8 - - - +
335O TRP* 1.3 74.0 + - - +
235U ASN 4.8 4.0 - - - +
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Residues in contact with TRP 335 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
289O ARG* 4.0 5.6 - - - +
318O GLY 4.7 10.8 - - - -
319O LEU 4.7 1.8 - - - -
320O VAL* 3.6 1.6 - - - -
321O LYS* 2.8 85.1 + - + +
333O MET 3.5 1.1 - - - -
334O THR* 1.3 92.2 - - - +
336O VAL* 1.3 91.0 + - - +
337O GLN* 3.5 31.9 - - + -
338O PRO* 4.8 4.5 - - + -
232U ASP* 5.4 3.4 - - - -
235U ASN* 3.9 32.8 - - + +
236U LEU* 5.7 8.2 - - + +
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Residues in contact with VAL 336 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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278O MET* 4.2 29.6 - - - +
281O THR* 3.7 27.4 - - - +
282O PHE* 5.2 8.7 - - + +
289O ARG* 4.1 20.7 - - - +
319O LEU 3.9 3.1 - - - -
320O VAL* 4.9 13.2 - - + -
333O MET* 4.9 6.7 - - + -
335O TRP* 1.3 87.5 - - - +
337O GLN* 1.3 75.8 + - - +
338O PRO* 3.5 0.5 - - - +
339O ARG* 4.4 9.2 - - - +
235U ASN* 2.9 24.3 + - - -
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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