Contacts of the helix formed by residues 384 - 395 (chain K) in PDB entry 1FQV
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 PRO 384 (chain K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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156I GLY 4.7 3.4 - - - +
158I ASN* 4.2 21.1 - - + +
181I PHE* 3.1 44.0 - - + -
362K PRO* 4.0 11.2 - - + -
382K ILE 3.7 7.0 - - - +
383K VAL* 1.3 81.4 - - + +
385K ASP* 1.3 69.0 + - - +
386K GLY 2.8 5.9 + - - +
387K THR* 2.9 29.7 + - + +
388K LEU* 2.8 19.2 + - - +
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Residues in contact with ASP 385 (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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156I GLY* 4.4 21.3 + - - +
181I PHE* 4.7 0.6 - - - -
383K VAL 3.5 2.9 + - - -
384K PRO* 1.3 70.5 - - - +
386K GLY* 1.3 59.7 + - - +
388K LEU* 3.5 14.0 - - - +
389K GLN* 3.3 31.4 + - - +
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Residues in contact with GLY 386 (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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156I GLY 5.6 0.6 + - - -
384K PRO* 2.8 8.6 + - - +
385K ASP* 1.3 73.4 - - - +
387K THR* 1.3 61.3 + - - +
388K LEU 2.9 5.2 + - - -
389K GLN* 3.2 6.7 + - - +
390K LEU* 3.2 26.0 + - - +
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Residues in contact with THR 387 (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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158I ASN* 5.9 5.4 - - + +
362K PRO* 4.3 5.7 - - - +
363K GLU* 3.7 22.0 - - - +
383K VAL* 3.6 5.3 - - - +
384K PRO* 2.9 38.6 + - + +
386K GLY* 1.3 75.6 - - - +
388K LEU* 1.3 56.1 + - - +
390K LEU* 3.7 15.6 - - + +
391K LEU* 2.8 30.1 + - - +
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Residues in contact with LEU 388 (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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379K VAL* 4.7 0.4 - - + -
383K VAL* 3.3 22.2 - - + +
384K PRO 2.8 18.1 + - - +
385K ASP* 3.5 16.4 - - - +
386K GLY 2.9 0.2 - - - -
387K THR* 1.3 80.3 + - - +
389K GLN* 1.3 68.6 + - - +
391K LEU* 3.3 6.7 + - + +
392K LYS* 3.0 39.2 + - - +
400K ILE* 3.6 23.3 - - + -
401K ASN* 3.4 35.7 - - + +
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Residues in contact with GLN 389 (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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385K ASP* 3.3 23.0 + - - +
386K GLY* 3.2 8.9 + - - +
388K LEU* 1.3 85.9 - - - +
390K LEU* 1.3 64.8 + - + +
392K LYS* 2.9 46.1 + - + +
393K GLU* 2.7 34.9 + - - +
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Residues in contact with LEU 390 (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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386K GLY 3.2 18.2 + - - +
387K THR* 3.7 16.6 - - + +
389K GLN* 1.3 76.4 - - + +
391K LEU* 1.3 58.6 + - - +
393K GLU* 2.8 36.6 + - + +
394K ALA* 2.8 15.9 + - - +
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Residues in contact with LEU 391 (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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362K PRO 4.8 4.3 - - - +
363K GLU 5.3 0.2 - - - +
365K LEU* 3.6 36.6 - - + +
366K LEU* 3.9 40.8 - - + +
377K LEU* 4.8 4.9 - - + -
379K VAL* 4.9 0.2 - - + -
383K VAL* 4.8 3.1 - - + -
387K THR 2.8 17.9 + - - +
388K LEU* 3.4 18.2 - - + +
389K GLN 3.2 0.2 - - - -
390K LEU* 1.3 77.1 - - - +
392K LYS* 1.3 56.4 + - - +
394K ALA* 3.3 5.8 + - - +
395K LEU* 2.9 33.4 + - + +
400K ILE* 3.8 22.2 - - + -
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Residues in contact with LYS 392 (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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388K LEU* 3.0 30.0 + - - +
389K GLN* 2.9 39.4 + - + +
390K LEU 3.2 0.2 - - - -
391K LEU* 1.3 72.4 - - - +
393K GLU* 1.3 69.9 + - - +
395K LEU 3.5 17.7 - - - +
396K PRO* 3.5 6.4 - - - +
400K ILE* 3.7 46.3 + - + +
401K ASN* 5.3 2.4 + - - -
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Residues in contact with GLU 393 (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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389K GLN* 2.7 29.0 + - - +
390K LEU* 2.8 27.0 + - + +
392K LYS* 1.3 82.0 - - - +
394K ALA* 1.3 63.7 + - - +
396K PRO* 3.3 13.0 - - - +
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Residues in contact with ALA 394 (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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366K LEU* 3.4 33.7 - - + -
390K LEU 2.8 10.0 + - - +
391K LEU* 3.6 7.0 - - - +
393K GLU* 1.3 78.9 - - - +
395K LEU* 1.3 63.7 + - + +
396K PRO* 2.8 11.8 - - - +
397K HIS* 5.2 0.2 - - - -
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Residues in contact with LEU 395 (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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365K LEU 4.2 17.0 - - - +
366K LEU* 4.2 15.5 - - + +
368K LEU* 4.7 0.7 - - + -
369K GLY* 3.8 24.5 - - - +
377K LEU* 5.6 1.1 - - + -
391K LEU* 2.9 26.8 + - + +
392K LYS* 3.5 10.5 - - - +
394K ALA* 1.3 86.2 - - + +
396K PRO* 1.3 60.4 - - - +
397K HIS* 3.1 27.8 - - + +
398K LEU* 3.0 43.7 + - + +
400K ILE* 4.7 3.0 - - + +
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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