Contacts of the helix formed by residues 322 - 327 (chain K) in PDB entry 3GOK
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 HIS 322 (chain K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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297K GLU* 3.9 27.1 + - + +
300K MET* 6.1 0.2 - - - +
301K LEU* 3.7 40.1 - - + +
314K MET* 4.4 9.6 - - + -
318K GLU 3.1 11.5 + - - +
319K PHE* 3.1 16.7 + - - +
321K ASN* 1.3 75.6 - - - +
323K PRO* 1.3 71.8 - - + +
324K TRP* 3.0 41.6 + - + +
325K ILE* 2.9 11.9 + - + +
326K MET 2.8 24.6 + - - -
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Residues in contact with PRO 323 (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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297K GLU* 3.7 21.8 - - - +
321K ASN 3.4 5.8 - - - +
322K HIS* 1.3 94.1 - - + +
324K TRP* 1.3 59.3 + - - +
326K MET* 3.9 9.9 - - + -
327K GLN* 3.1 40.3 + - - +
330K LYS* 5.8 0.3 - - - +
331K VAL* 5.1 0.3 - - - +
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Residues in contact with TRP 324 (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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160K GLU* 3.1 44.9 + - + -
163K ALA* 4.0 9.6 - - + -
164K SER* 2.8 46.6 + - - -
167K MET* 4.2 4.9 - - + -
253K MET* 4.0 23.1 - - + -
257K LEU* 4.5 5.2 - - + -
295K SER* 5.0 0.2 - - - -
297K GLU* 3.7 16.2 + - - +
298K VAL* 3.2 35.4 - - + +
301K LEU* 4.0 11.7 - - + -
322K HIS* 3.0 24.7 + - + +
323K PRO* 1.3 77.5 - - - +
325K ILE* 1.3 89.9 - - + +
328K SER* 4.2 1.4 - - - -
331K VAL* 3.5 27.2 - - + +
332K PRO* 5.8 0.9 - - + -
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Residues in contact with ILE 325 (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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164K SER* 4.3 3.8 - - - +
167K MET* 3.9 12.8 - - + -
168K LYS* 3.5 34.6 - - + +
301K LEU* 4.6 6.3 - - + -
319K PHE* 3.6 49.4 - - + +
320K MET* 4.2 22.0 - - + +
322K HIS* 2.9 8.2 + - + +
324K TRP* 1.3 105.6 - - + +
326K MET* 1.3 67.4 + - - +
327K GLN 3.4 0.2 - - - -
328K SER* 3.1 19.2 + - - -
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Residues in contact with MET 326 (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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168K LYS* 4.0 15.3 + - - +
320K MET 3.6 14.1 + - - +
321K ASN* 3.0 48.9 - - - +
322K HIS 2.8 9.6 + - - +
323K PRO* 3.9 9.4 - - + -
325K ILE* 1.3 79.9 - - - +
327K GLN* 1.3 68.2 + - + +
328K SER 3.7 1.9 + - - -
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Residues in contact with GLN 327 (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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323K PRO* 3.1 29.8 + - - +
324K TRP 4.4 0.9 - - - -
325K ILE 4.3 0.4 - - - -
326K MET* 1.3 86.3 - - + +
328K SER* 1.3 63.4 + - - +
329K THR* 3.1 6.3 - - - +
330K LYS* 3.1 52.8 + - + +
331K VAL* 3.5 13.3 + - - +
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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