Contacts of the helix formed by residues 411 - 423 (chain C) in PDB entry 6VVT
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 411 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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144C PHE* 2.9 35.2 - - + +
145C MET* 3.1 57.7 - - + +
146C GLY* 4.2 1.3 - - - +
387C MET* 5.6 1.1 - - - -
409C ILE* 3.4 22.1 + - + -
410C ASN* 1.3 68.5 - - - +
412C ARG* 1.3 66.8 + - - +
413C PRO* 3.3 2.5 - - - -
414C VAL* 2.8 20.7 + - + +
415C VAL* 3.0 17.2 + - + +
322F ARG* 5.7 5.5 - - + +
325F LEU* 5.2 13.5 - - + -
326F GLN* 3.4 17.5 - - - +
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Residues in contact with ARG 412 (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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410C ASN* 2.9 21.6 + - - +
411C ILE* 1.3 78.7 - - - +
413C PRO* 1.3 62.4 - - + +
415C VAL* 3.4 9.4 - - - +
416C ALA* 2.9 34.8 + - - +
322F ARG* 4.4 15.2 - - + +
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Residues in contact with PRO 413 (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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383C GLY* 3.9 8.3 - - - +
386C ARG* 4.7 16.8 - - + +
387C MET* 4.5 21.1 - - + +
390C VAL* 5.0 9.0 - - + -
410C ASN* 2.9 29.8 - - - +
411C ILE 3.4 0.4 - - - -
412C ARG* 1.3 83.3 - - + +
414C VAL* 1.3 56.9 + - - +
416C ALA* 4.1 5.1 - - + -
417C ALA* 3.1 26.3 + - - +
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Residues in contact with VAL 414 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145C MET* 4.0 36.6 - - + +
380C ILE* 5.7 7.4 - - + +
383C GLY* 3.3 32.3 - - - +
384C LEU* 4.2 12.6 - - + -
387C MET* 3.8 17.9 - - + -
411C ILE* 2.8 21.2 + - + +
413C PRO* 1.3 70.5 - - - +
415C VAL* 1.3 66.4 + - - +
417C ALA* 3.0 17.2 + - - +
418C ILE* 3.4 16.1 + - + +
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Residues in contact with VAL 415 (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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145C MET 4.1 13.7 + - - +
146C GLY* 4.8 11.0 - - - -
147C ASP* 5.2 11.0 - - - +
411C ILE* 3.0 15.8 + - + +
412C ARG* 3.4 17.0 - - - +
414C VAL* 1.3 79.1 - - - +
416C ALA* 1.3 63.3 + - + +
418C ILE* 3.0 35.2 - - + +
419C LYS* 3.1 15.2 + - + +
325F LEU* 5.6 9.6 - - + -
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Residues in contact with ALA 416 (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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412C ARG* 2.9 21.8 + - + +
413C PRO* 4.4 5.2 - - + -
415C VAL* 1.3 79.4 - - + +
417C ALA* 1.3 57.0 + - - +
419C LYS* 4.0 8.4 - - + +
420C GLU* 2.9 32.1 + - + +
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Residues in contact with ALA 417 (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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379C GLN* 3.1 48.2 + - - +
380C ILE* 5.7 0.4 - - - -
382C VAL* 5.4 4.3 - - + -
383C GLY* 4.2 10.3 - - - +
413C PRO 3.1 20.0 + - - +
414C VAL 3.0 7.9 + - - +
416C ALA* 1.3 76.7 - - - +
418C ILE* 1.3 64.3 + - + +
420C GLU* 3.5 3.7 + - - +
421C PHE 3.2 10.6 + - - -
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Residues in contact with ILE 418 (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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124C LEU* 6.2 1.8 - - + -
145C MET 5.8 1.6 - - - +
146C GLY 5.8 2.0 - - - -
147C ASP 4.2 19.3 - - - +
148C PHE* 4.5 21.8 - - + -
149C PRO* 4.7 7.4 - - + -
376C ILE* 5.7 6.1 - - + +
379C GLN* 4.8 7.0 - - + -
380C ILE* 4.2 25.8 - - + -
414C VAL* 3.6 11.9 - - + +
415C VAL* 3.0 34.5 - - + +
417C ALA* 1.3 73.7 - - + +
419C LYS* 1.3 64.9 + - + +
421C PHE* 3.0 15.7 + - - +
422C PHE* 3.1 34.2 + - + -
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Residues in contact with LYS 419 (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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159C ILE* 5.8 4.0 - - + +
160C ASN* 5.7 9.4 - - - +
415C VAL* 3.1 22.6 + - + +
416C ALA* 4.2 7.0 - - - +
418C ILE* 1.3 78.2 - - - +
420C GLU* 1.3 59.4 + - - +
421C PHE 3.4 0.5 + - - -
422C PHE* 5.0 2.2 - - - +
423C GLY* 3.6 17.0 + - - -
424C THR* 5.8 0.3 - - - +
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Residues in contact with GLU 420 (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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379C GLN* 4.9 6.3 + - - +
416C ALA* 2.9 23.3 + - + +
417C ALA* 3.7 8.5 - - - +
418C ILE 3.1 0.2 - - - -
419C LYS* 1.3 76.9 - - - +
421C PHE* 1.3 54.2 + - - +
423C GLY 2.6 18.5 - - - +
424C THR* 2.7 16.2 + - + +
425C SER* 4.1 2.1 + - - -
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Residues in contact with PHE 421 (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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166C VAL* 4.2 28.0 - - + -
375C LEU* 4.2 22.4 - - + -
376C ILE* 3.1 36.6 - - + -
379C GLN* 3.8 29.6 - - + +
417C ALA 3.2 11.2 + - - +
418C ILE* 3.0 12.1 + - + +
420C GLU* 1.3 74.7 - - - +
422C PHE* 1.3 86.0 + + - +
423C GLY 2.7 8.0 + - - +
425C SER* 2.7 45.8 - - - -
427C LEU* 4.8 12.3 - - + -
428C SER* 3.8 3.1 - - - -
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Residues in contact with PHE 422 (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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52C PHE* 5.4 1.8 - + - -
148C PHE* 6.5 0.7 - + - -
149C PRO* 3.4 32.8 - - + -
157C PHE* 3.6 49.1 - + + -
159C ILE* 3.7 35.0 - - + -
164C ARG* 2.6 23.5 + - + -
166C VAL* 4.1 15.9 - - + -
376C ILE* 3.6 27.8 - - + -
418C ILE* 3.1 24.9 + - + +
419C LYS* 5.0 2.0 - - - +
421C PHE* 1.3 87.2 - + - +
423C GLY* 1.3 49.7 + - - +
428C SER* 2.3 28.8 + - - -
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Residues in contact with GLY 423 (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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159C ILE* 4.9 4.3 - - - +
164C ARG* 3.9 11.4 - - - -
419C LYS 3.6 12.3 + - - -
420C GLU 2.6 17.0 - - - +
421C PHE 2.7 3.3 + - - +
422C PHE* 1.3 75.7 - - - +
424C THR* 1.3 77.9 + - - +
425C SER 2.7 9.1 + - - -
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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