Contacts of the helix formed by residues 361 - 370 (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 ILE 361 (chain K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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183I ASP* 5.6 7.0 - - - +
337K ASN* 5.4 2.8 - - - +
359K ASP 3.5 7.0 + - - +
360K ILE* 1.3 71.1 - - - +
362K PRO* 1.3 71.4 - - + +
363K GLU* 3.3 29.6 - - + +
364K THR* 2.5 46.9 + - + +
365K LEU 3.7 1.0 + - - -
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Residues in contact with PRO 362 (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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181I PHE* 5.4 2.7 - - + -
183I ASP* 5.5 7.4 - - - +
360K ILE 3.2 7.1 - - - +
361K ILE* 1.3 87.9 - - + +
363K GLU* 1.3 75.0 + - - +
365K LEU* 3.2 33.3 - - + +
366K LEU 4.6 0.2 + - - -
382K ILE* 2.8 29.6 - - + +
383K VAL* 4.6 4.6 - - + +
384K PRO* 4.0 21.3 - - + -
387K THR* 4.3 7.1 - - - +
391K LEU* 4.8 4.3 - - - +
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Residues in contact with GLU 363 (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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183I ASP* 5.8 0.3 - - - +
361K ILE* 2.9 22.3 + - + +
362K PRO* 1.3 82.9 - - - +
364K THR* 1.3 67.6 + - + +
365K LEU 2.9 3.0 + - - -
366K LEU* 3.0 21.3 + - - +
367K GLU* 5.6 0.2 - - - +
384K PRO* 6.0 0.2 - - - +
387K THR* 3.7 26.4 - - - +
391K LEU* 5.3 1.0 - - - +
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Residues in contact with THR 364 (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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337K ASN* 3.2 49.4 - - + +
340K PHE* 3.2 5.3 - - - -
360K ILE* 3.7 9.2 - - - +
361K ILE* 2.5 43.6 + - + +
363K GLU* 1.3 77.3 - - + +
365K LEU* 1.3 62.0 + - - +
366K LEU 2.8 2.1 + - - -
367K GLU* 2.9 31.7 + - - +
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Residues in contact with LEU 365 (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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340K PHE* 4.1 6.3 - - + -
354K LEU* 5.0 2.0 - - + -
360K ILE* 3.8 24.2 - - + -
362K PRO* 3.2 24.0 - - + +
363K GLU 2.9 1.0 + - - -
364K THR* 1.3 78.3 + - - +
366K LEU* 1.3 58.9 + - - +
367K GLU 3.1 0.4 - - - -
368K LEU* 3.2 36.7 + - + +
377K LEU* 4.7 2.8 - - + +
379K VAL* 3.8 26.7 - - + -
382K ILE* 4.4 3.8 - - + -
383K VAL* 3.3 34.3 - - + -
391K LEU* 3.6 26.8 - - + +
395K LEU* 4.2 5.4 - - - +
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Residues in contact with LEU 366 (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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363K GLU 3.0 13.2 + - - +
364K THR 2.8 0.8 + - - -
365K LEU* 1.3 78.3 - - - +
367K GLU* 1.3 62.8 + - + +
369K GLY* 3.1 15.2 + - - -
370K GLU* 5.5 0.2 - - - +
391K LEU* 3.9 14.9 - - + +
394K ALA* 3.4 32.5 - - + -
395K LEU* 4.2 14.9 - - + +
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Residues in contact with GLU 367 (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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337K ASN* 3.2 31.3 + - - +
340K PHE* 3.9 17.2 - - + +
344K PHE* 3.5 11.9 - - + -
364K THR* 2.9 26.2 + - - +
366K LEU* 1.3 73.7 - - + +
368K LEU* 1.3 57.0 + - - +
369K GLY 2.7 11.8 + - - -
370K GLU* 2.8 33.1 - - + +
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Residues in contact with LEU 368 (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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340K PHE* 3.6 41.3 - - + -
343K PHE* 4.3 8.5 - - + -
344K PHE* 4.4 4.0 - - + -
352K LEU* 4.3 4.7 - - + -
354K LEU* 4.0 11.4 - - + -
365K LEU* 3.2 27.1 + - + +
366K LEU 3.2 1.6 - - - -
367K GLU* 1.3 76.0 - - - +
369K GLY* 1.3 59.2 + - - +
370K GLU 3.0 3.8 + - - +
371K ILE* 3.5 28.2 + - + +
374K LEU* 3.7 25.8 - - + +
377K LEU* 3.8 39.3 - - + -
395K LEU* 4.7 4.3 - - + -
397K HIS* 5.2 0.3 - - - -
398K LEU* 4.8 1.0 - - - +
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Residues in contact with GLY 369 (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 3.1 12.7 + - - -
367K GLU 2.7 3.8 + - - -
368K LEU* 1.3 77.6 - - - +
370K GLU* 1.3 68.5 + - - +
371K ILE 3.4 5.3 - - - +
372K PRO* 4.8 1.0 - - - +
395K LEU* 3.8 24.8 - - - +
397K HIS* 4.5 12.2 + - - -
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Residues in contact with GLU 370 (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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344K PHE* 3.2 35.0 - - + -
366K LEU 5.5 0.2 - - - +
367K GLU* 2.8 26.6 + - + +
369K GLY* 1.3 82.4 - - - +
371K ILE* 1.3 61.2 + - - +
372K PRO* 2.7 22.5 - - - +
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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