Contacts of the helix formed by residues 391 - 403 (chain C) in PDB entry 6CP3
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 SER 391 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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390C GLY* 1.3 78.7 - - - +
392C LEU* 1.3 58.0 + - - +
393C LYS* 3.4 2.5 - - - +
394C LEU* 4.1 20.4 - - - +
395C PHE* 2.9 27.2 + - - +
425D THR 5.9 2.2 - - - -
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Residues in contact with LEU 392 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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157C ALA* 4.7 6.3 - - + +
158C LEU* 4.3 15.5 - - + -
389C ALA* 3.6 25.7 + - + +
391C SER* 1.3 75.3 - - - +
393C LYS* 1.3 61.0 + - - +
395C PHE* 3.2 9.5 + - + +
396C LEU* 2.9 42.4 + - + +
426C LEU* 3.7 34.8 - - + -
430C LEU* 6.1 4.9 - - + -
447C ILE* 4.0 35.0 - - + -
451C VAL* 4.0 16.2 - - + -
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Residues in contact with LYS 393 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157C ALA 5.5 1.1 + - - +
158C LEU* 3.7 38.7 - - + +
159C VAL* 4.7 1.3 - - - -
369C VAL* 4.4 23.3 + - + +
370C GLY 6.1 0.2 - - - -
372C SER 3.4 22.1 + - - -
373C VAL* 3.7 27.7 - - - +
374C SER 5.3 1.1 - - - +
389C ALA 5.2 0.8 + - - -
391C SER* 3.4 0.6 - - - -
392C LEU* 1.3 78.2 - - - +
394C LEU* 1.3 72.8 + - + +
396C LEU* 3.2 5.4 + - - +
397C ALA* 3.0 25.3 + - + +
345D TYR* 5.0 6.9 + - - -
600D ADP 5.9 1.0 + - - -
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Residues in contact with LEU 394 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
390C GLY 6.1 0.2 - - - +
391C SER* 3.8 19.8 + - - +
393C LYS* 1.3 92.8 - - + +
395C PHE* 1.3 58.4 + - - +
397C ALA* 3.6 7.1 - - + +
398C GLN* 2.9 36.4 + - + +
343D GLY* 4.3 24.9 - - - +
345D TYR* 4.8 14.6 - - + -
424D PHE 5.3 3.1 - - - +
425D THR* 4.5 25.8 - - + -
458D TYR* 4.1 21.3 - - + +
459D MET* 4.8 2.5 - - + -
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Residues in contact with PHE 395 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
391C SER* 2.9 23.1 + - - +
392C LEU* 3.4 13.5 - - + +
393C LYS 3.2 0.4 - - - -
394C LEU* 1.3 75.1 - - - +
396C LEU* 1.3 63.2 + - + +
398C GLN* 3.8 3.5 - - + -
399C TYR* 2.8 32.7 + - + +
419C THR* 3.8 39.3 - - + -
422C ARG* 3.4 39.3 - - - -
423C GLY* 3.9 15.0 - - - -
426C LEU* 3.9 29.6 - - + -
451C VAL* 6.3 0.4 - - + -
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Residues in contact with LEU 396 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158C LEU* 5.0 4.0 - - + -
369C VAL* 4.1 34.8 - - + -
392C LEU* 2.9 47.0 + - + +
393C LYS 3.2 5.8 + - - +
395C PHE* 1.3 80.9 - - + +
397C ALA* 1.3 61.6 + - - +
399C TYR* 3.4 14.1 - - + +
400C ARG* 2.9 39.5 + - - +
423C GLY* 5.3 0.9 - - - +
426C LEU* 4.5 13.0 - - + -
427C THR* 4.0 28.0 - - + +
430C LEU* 5.1 11.4 - - + -
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Residues in contact with ALA 397 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
369C VAL* 5.5 2.8 - - - +
370C GLY* 5.6 8.5 - - - -
393C LYS* 3.0 15.0 + - + +
394C LEU* 3.6 15.5 - - + +
395C PHE 3.3 0.2 - - - -
396C LEU* 1.3 76.2 - - - +
398C GLN* 1.3 58.4 + - - +
400C ARG* 3.8 8.6 - - - +
401C GLU* 2.9 26.0 + - - +
340D SER 5.8 0.2 - - - +
341D GLU 4.6 14.6 - - - +
342D LEU 5.1 0.9 - - - -
343D GLY* 4.5 20.4 - - - -
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Residues in contact with GLN 398 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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394C LEU* 2.9 21.7 + - + +
395C PHE* 4.4 3.8 - - + +
397C ALA* 1.3 73.6 - - + +
399C TYR* 1.3 59.1 + - - +
401C GLU* 3.3 22.8 + - - +
402C VAL* 2.9 37.8 + - + +
342D LEU 3.9 11.2 + - - +
343D GLY* 5.0 1.7 - - - -
412D ARG* 5.1 7.9 - - - +
455D HIS* 3.5 28.7 + - - -
458D TYR* 3.3 49.6 + - - +
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Residues in contact with TYR 399 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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395C PHE* 2.8 28.8 + - + +
396C LEU* 3.4 13.9 - - + +
397C ALA 3.2 0.2 - - - -
398C GLN* 1.3 77.4 - - - +
400C ARG* 1.3 81.8 + - + +
402C VAL* 3.8 2.4 - - - +
403C ALA* 2.8 37.3 + - + +
419C THR* 3.8 12.8 - - - +
420C LEU* 3.6 29.6 - - + +
423C GLY* 3.5 22.7 - - - -
424C GLU* 3.4 33.3 - - - +
427C THR* 3.5 24.6 + - + +
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Residues in contact with ARG 400 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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358C LEU* 6.1 4.7 - - - -
368C ASN* 3.6 13.0 + - - -
369C VAL* 3.9 10.3 - - - +
370C GLY* 3.0 38.8 - - - +
396C LEU* 2.9 26.1 + - - +
397C ALA* 4.3 3.4 - - - +
399C TYR* 1.3 98.6 - - + +
401C GLU* 1.3 65.6 + - - +
403C ALA* 3.9 7.0 - - + -
404C ALA* 3.5 16.8 + - - +
427C THR* 5.7 4.7 + - - -
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Residues in contact with GLU 401 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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397C ALA 2.9 12.5 + - - +
398C GLN* 3.3 26.1 + - - +
400C ARG* 1.3 80.2 - - - +
402C VAL* 1.3 64.5 + - + +
404C ALA* 3.4 15.5 + - - +
405C PHE* 4.4 10.1 + - + -
341D GLU 5.6 0.7 - - - +
342D LEU* 3.1 57.0 - - + +
408D ARG* 5.4 1.1 - - - +
412D ARG* 2.3 40.2 + - - +
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Residues in contact with VAL 402 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
398C GLN* 2.9 25.2 + - + +
399C TYR* 4.2 2.9 - - - +
401C GLU* 1.3 80.0 - - + +
403C ALA* 1.3 56.9 + - - +
404C ALA 3.1 0.2 - - - -
405C PHE* 3.0 38.2 + - + +
406C ALA* 3.9 3.3 + - - +
412C LEU* 5.3 7.9 - - + +
416C THR* 4.5 27.8 - - + +
419C THR* 5.1 7.4 - - - +
420C LEU* 6.6 0.4 - - + -
408D ARG* 4.8 12.8 - - - +
412D ARG* 5.1 1.8 - - - +
454D GLU* 6.0 0.2 - - - +
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Residues in contact with ALA 403 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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399C TYR* 2.8 31.3 + - + +
400C ARG* 4.0 9.4 - - + -
401C GLU 3.3 0.2 - - - -
402C VAL* 1.3 74.5 - - - +
404C ALA* 1.3 58.8 + - - +
405C PHE 3.2 0.6 + - - -
406C ALA* 3.7 6.7 + - - +
407C GLN* 2.7 40.6 + - - +
420C LEU* 4.0 27.4 - - + -
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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