Contacts of the strand formed by residues 340 - 346 (chain K) in PDB entry 3GHG
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 ILE 340 (chain K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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310K LEU* 6.1 1.1 - - + -
329K PHE* 4.2 13.9 - - + -
330K THR 3.5 3.6 - - - -
331K VAL* 4.5 0.7 - - - +
339K GLN* 1.3 78.9 - - - +
341K SER* 1.3 67.0 + - - +
342K VAL* 3.8 26.9 - - + -
353K LEU* 5.6 5.6 - - + -
370K HIS* 3.7 18.6 - - + +
371K ASN* 5.5 0.7 - - - -
372K GLY* 2.9 28.6 + - - +
373K MET 3.1 6.9 + - - +
402K TRP* 6.3 0.7 - - + -
403K TRP* 3.1 74.0 - - + -
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Residues in contact with SER 341 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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328K GLY 5.7 0.3 - - - -
329K PHE* 3.3 4.7 + - - -
330K THR* 3.0 43.6 + - - +
339K GLN* 6.1 0.9 - - - -
340K ILE* 1.3 74.7 - - - +
342K VAL* 1.3 69.1 + - - +
343K ASN* 5.4 4.4 + - - -
371K ASN* 3.2 12.8 - - - -
372K GLY* 4.9 1.3 - - - -
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Residues in contact with VAL 342 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
310K LEU* 5.5 2.2 - - + -
326K TYR* 3.2 37.7 - - + -
328K GLY 3.2 11.0 - - - +
329K PHE* 4.3 9.0 - - + -
340K ILE* 3.8 25.1 - - + -
341K SER* 1.3 82.4 - - - +
343K ASN* 1.3 65.6 + - - +
353K LEU* 3.7 23.8 - - + -
354K MET* 3.5 13.0 - - + +
370K HIS* 6.6 0.2 - - + -
371K ASN* 2.8 35.7 + - - +
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Residues in contact with ASN 343 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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326K TYR* 3.3 6.4 - - - -
327K GLY 3.1 14.2 + - - -
328K GLY* 3.0 19.8 + - - -
341K SER* 5.4 4.0 + - - -
342K VAL* 1.3 76.9 + - - +
344K LYS* 1.3 98.8 - - + +
345K TYR 3.5 1.8 - - - -
354K MET* 3.2 17.9 - - - -
371K ASN* 4.9 1.6 - - - +
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Residues in contact with LYS 344 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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325K HIS 3.6 1.7 - - - +
327K GLY* 3.1 28.8 + - - +
328K GLY* 4.3 10.7 - - - +
343K ASN* 1.3 101.9 - - - +
345K TYR* 1.3 64.6 + - - +
346K ARG* 4.5 5.4 - - - +
354K MET* 3.8 4.0 - - - +
457K PHE* 4.6 18.6 - - + -
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Residues in contact with TYR 345 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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324K ALA* 4.3 6.5 - - + -
325K HIS 3.0 24.0 - - - -
326K TYR* 3.4 29.2 - + + -
344K LYS* 1.3 78.3 - - - +
346K ARG* 1.3 80.5 + - - +
347K GLY 2.8 35.1 + - - -
349K ALA 4.0 0.2 + - - -
350K GLY* 2.8 26.4 + - - -
351K ASN* 3.0 42.6 - - + +
354K MET* 3.1 13.8 - - + +
355K ASP* 5.2 0.2 - - - -
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Residues in contact with ARG 346 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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245K GLU* 5.1 9.5 + - - -
309K GLU* 5.1 2.0 + - - -
325K HIS* 2.8 80.2 + - + +
344K LYS 4.5 5.6 - - - +
345K TYR* 1.3 88.6 - - - +
347K GLY* 1.3 58.5 + - - +
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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