Contacts of the helix formed by residues 392 - 400 (chain C) in PDB entry 6V99
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 ASP 392 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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391C GLU* 1.3 84.4 - - + +
393C PRO* 1.3 59.7 - - - +
394C GLU* 2.7 27.9 - - - +
395C LEU* 3.2 35.5 + - + +
396C ASP* 2.9 38.8 + - - +
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Residues in contact with PRO 393 (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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390C GLY 6.0 0.7 - - - +
391C GLU 3.5 10.8 - - - +
392C ASP* 1.3 85.1 - - - +
394C GLU* 1.3 73.1 + - + +
396C ASP* 3.4 1.7 + - - +
397C ALA* 2.8 30.1 + - - +
402C ARG* 3.6 41.6 + - - +
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Residues in contact with GLU 394 (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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392C ASP* 2.7 23.2 - - - +
393C PRO* 1.3 88.5 - - + +
395C LEU* 1.3 64.0 + - - +
397C ALA* 3.8 6.5 - - - +
398C LYS* 3.1 23.2 + - - +
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Residues in contact with LEU 395 (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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388C ILE 5.4 2.5 - - - +
392C ASP* 3.2 34.0 + - + +
393C PRO 3.4 0.4 - - - -
394C GLU* 1.3 76.1 - - - +
396C ASP* 1.3 69.3 + - - +
398C LYS* 3.2 7.6 + - + +
399C ARG* 3.0 61.6 + - + +
420C LEU* 3.8 29.6 - - + +
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Residues in contact with ASP 396 (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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388C ILE 4.0 6.2 - - - +
389C VAL* 3.9 13.9 - - - +
390C GLY* 2.8 38.3 + - - -
391C GLU 3.7 1.7 + - - -
392C ASP 2.9 28.7 + - - +
393C PRO* 3.8 5.0 - - - +
395C LEU* 1.3 83.0 - - - +
397C ALA* 1.3 62.6 + - - +
399C ARG* 4.7 1.1 + - - -
400C PHE* 3.0 38.1 + - + +
402C ARG* 4.1 8.8 + - - +
408C CYS* 3.7 19.2 - - - -
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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
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393C PRO 2.8 17.0 + - - +
394C GLU* 3.8 8.3 - - - +
395C LEU 3.2 0.2 - - - -
396C ASP* 1.3 77.6 - - - +
398C LYS* 1.3 59.1 + - - +
400C PHE 2.9 19.1 - - - +
402C ARG* 3.8 22.2 - - + +
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Residues in contact with LYS 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 GLU 3.1 17.8 + - - +
395C LEU* 3.2 8.0 + - + +
397C ALA* 1.3 77.7 - - - +
399C ARG* 1.3 62.8 + - + +
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Residues in contact with ARG 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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387C LEU* 3.7 25.3 - - - +
388C ILE 4.1 11.5 + - - +
395C LEU* 3.0 48.6 + - + +
396C ASP* 5.4 0.8 + - - +
398C LYS* 1.3 80.8 - - + +
400C PHE* 1.3 90.7 + - + +
414C MET* 3.8 18.4 - - - +
418C LEU* 3.6 26.9 - - + +
420C LEU* 2.7 51.3 + - - +
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Residues in contact with PHE 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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387C LEU* 4.2 9.9 - - + -
388C ILE 5.2 1.3 - - - -
389C VAL* 3.5 38.1 - - + -
396C ASP* 3.0 24.3 + - - +
397C ALA 2.9 17.8 - - - +
398C LYS 4.9 0.2 - - - +
399C ARG* 1.3 106.8 - - + +
401C ARG* 1.3 67.0 + - - +
402C ARG 3.5 2.6 + - - -
408C CYS* 4.5 7.6 - - + -
409C LEU 3.7 5.2 - - - +
410C ILE* 4.0 14.4 - - + -
414C MET* 3.1 35.4 - - + -
415C ILE* 3.8 21.8 - - + -
418C LEU* 4.1 17.0 - - + -
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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