Contacts of the helix formed by residues 400 - 409 (chain C) in PDB entry 6P19
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 VAL 400 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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152C SER* 4.9 2.5 - - - -
153C PRO* 4.5 20.2 - - + -
179C TYR* 5.7 7.0 - - + -
397C LEU 4.6 1.1 - - - +
398C SER 2.9 8.5 + - - +
399C ALA* 1.3 79.4 - - + +
401C GLY* 1.3 64.2 + - - +
402C ARG 3.2 0.9 - - - -
403C MET* 3.2 7.6 + - + +
404C LYS* 3.0 28.5 + - + +
452C ARG* 3.8 37.5 - - - +
584C TYR* 4.2 21.1 - - + +
586C PHE* 4.7 10.5 - - + -
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Residues in contact with GLY 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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153C PRO* 3.5 30.6 - - - +
154C GLY* 4.3 3.5 - - - -
397C LEU* 3.1 23.7 + - - +
400C VAL* 1.3 80.6 - - - +
402C ARG* 1.3 58.3 + - - +
404C LYS* 4.1 0.6 - - - +
405C PHE* 2.8 32.8 + - - +
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Residues in contact with ARG 402 (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 LEU* 3.5 17.3 + - + +
398C SER* 4.6 4.0 - - - +
399C ALA* 3.8 21.3 - - - +
400C VAL 3.2 1.0 - - - +
401C GLY* 1.3 75.6 - - - +
403C MET* 1.3 63.0 + - - +
405C PHE* 3.3 34.2 - - - -
406C ASN* 3.2 32.0 + - - +
411C ARG* 5.5 1.0 - - - +
414C ILE 4.5 3.5 - - - +
415C GLU* 3.4 39.3 - - - +
416C GLY* 4.0 4.3 - - - +
417C SER* 2.5 36.8 + - - +
418C GLY 4.4 1.0 - - - -
419C ILE 2.8 27.3 + - - +
420C LEU* 4.9 3.6 - - - +
424C ASP* 4.4 12.1 + - - -
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Residues in contact with MET 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 ALA 4.3 5.8 - - - +
400C VAL* 3.2 17.6 + - + +
402C ARG* 1.3 80.4 - - - +
404C LYS* 1.3 85.6 + - + +
406C ASN* 3.9 0.9 - - - +
407C ARG* 2.9 60.8 + - + +
414C ILE* 4.1 24.9 + - + +
584C TYR* 3.7 37.7 - - + +
586C PHE* 4.2 18.8 - - + -
609C ILE* 5.1 11.0 - - + -
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Residues in contact with LYS 404 (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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152C SER* 3.8 19.3 - - - +
153C PRO 3.7 16.8 - - - +
154C GLY* 4.7 3.6 - - - -
155C VAL 5.6 2.2 - - - +
156C PHE* 4.9 9.2 - - + -
400C VAL* 3.0 15.9 + - + +
403C MET* 1.3 93.5 - - + +
405C PHE* 1.3 58.0 + - - +
407C ARG* 4.5 6.8 + - + +
408C SER* 2.8 39.6 + - - +
449C GLY 3.2 22.6 + - - -
450C ASN* 4.0 11.7 + - - -
586C PHE* 4.1 15.9 - - + -
609C ILE* 4.7 18.4 - - + +
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Residues in contact with PHE 405 (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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154C GLY* 4.9 5.1 - - - -
155C VAL* 3.6 31.4 - - + +
176C ILE* 5.1 2.7 - - + -
397C LEU* 5.4 6.1 - - + -
401C GLY 2.8 20.0 + - - +
402C ARG* 3.3 25.8 - - - +
403C MET 3.3 0.2 - - - -
404C LYS* 1.3 77.6 - - - +
406C ASN* 1.3 61.8 + - - +
408C SER* 3.7 3.2 - - - -
409C LEU* 2.9 52.7 + - + +
411C ARG* 4.4 0.4 - - - -
420C LEU* 4.4 16.2 - - + -
424C ASP* 3.4 42.2 - - + -
428C VAL* 3.5 26.5 - - + -
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Residues in contact with ASN 406 (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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402C ARG* 3.2 28.7 + - - +
403C MET 4.1 2.0 - - - +
405C PHE* 1.3 86.1 - - - +
407C ARG* 1.3 58.4 + - + +
408C SER 3.2 0.2 - - - -
409C LEU* 3.2 11.1 + - - +
411C ARG* 3.0 54.2 + - + +
413C GLU* 2.8 57.1 + - - +
414C ILE* 5.0 0.9 - - - -
415C GLU 3.7 12.3 + - - -
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Residues in contact with ARG 407 (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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403C MET* 2.9 41.5 + - + +
404C LYS* 3.7 7.6 - - + +
406C ASN* 1.3 77.3 - - + +
408C SER* 1.3 57.1 + - - +
410C LEU* 4.3 7.9 + - - +
411C ARG 4.8 9.0 - - - +
412C GLU 5.4 3.4 - - - +
413C GLU 5.6 0.2 - - - +
414C ILE* 4.6 14.8 - - + -
609C ILE* 3.9 33.5 - - - +
610C GLU* 5.1 11.3 + - - +
613C ASN* 6.0 1.4 - - - +
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Residues in contact with SER 408 (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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155C VAL* 4.2 21.7 + - - +
157C PHE* 4.1 12.8 - - - -
404C LYS* 2.8 24.6 + - - -
405C PHE 3.7 2.5 - - - -
407C ARG* 1.3 76.3 - - - +
409C LEU* 1.3 58.9 + - - +
410C LEU* 3.2 7.0 + - - -
431C LYS* 2.4 43.6 + - - +
443C ASP* 4.6 6.1 + - - -
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Residues in contact with LEU 409 (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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155C VAL* 5.5 2.0 - - + -
157C PHE* 5.4 2.9 - - + -
405C PHE* 2.9 47.2 + - + +
406C ASN 3.2 3.5 + - - +
408C SER* 1.3 79.3 - - - +
410C LEU* 1.3 70.6 + - - +
411C ARG* 3.1 45.0 + - - +
424C ASP 4.3 1.8 - - - +
427C ASP* 3.7 41.1 - - + +
428C VAL* 4.2 5.8 - - + +
431C LYS* 4.5 14.1 - - + -
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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