Contacts of the helix formed by residues 435 - 443 (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 ASN 435 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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433C GLN* 3.6 4.2 - - - +
434C ASN* 1.3 89.4 + - - +
436C PRO* 1.3 76.9 - - + +
437C LEU* 2.8 17.8 + - - +
438C SER* 2.5 49.5 + - - -
439C GLY 3.4 2.3 + - - -
603C GLN 3.4 4.8 + - - -
604C ARG* 2.8 41.4 + - - +
606C ALA 3.5 8.9 + - - +
608C PRO* 4.8 0.4 - - - -
631C ASP* 4.9 0.9 - - - -
698C CYS* 3.9 7.6 - - - -
706C LEU* 3.6 21.3 - - + -
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Residues in contact with PRO 436 (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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431C MET* 5.8 0.5 - - - +
433C GLN* 6.4 0.2 - - + -
435C ASN* 1.3 87.1 - - + +
437C LEU* 1.3 60.8 + - - +
439C GLY* 3.6 1.8 + - - -
440C LEU* 3.2 21.3 + - - +
626C ALA 5.4 0.7 - - - +
629C ALA* 3.6 21.1 - - + +
631C ASP* 3.7 36.3 - - + +
697C PRO* 4.0 16.8 - - + -
698C CYS* 3.7 26.2 - - + +
699C THR* 4.5 6.3 - - + -
704C MET* 3.8 20.2 - - + -
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Residues in contact with LEU 437 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
435C ASN* 2.8 16.2 + - - +
436C PRO* 1.3 72.7 - - - +
438C SER* 1.3 64.4 + - - +
440C LEU* 3.0 9.5 + - + +
441C THR* 2.9 45.9 + - + +
580C VAL* 5.1 7.2 - - + -
581C ALA* 3.8 22.4 - - + +
584C MET* 3.4 33.9 - - + -
603C GLN* 4.7 7.9 - - + +
604C ARG* 4.3 12.3 - - + +
625C ALA* 5.7 1.8 - - + -
629C ALA* 5.5 0.2 - - - -
704C MET* 3.4 17.4 - - + +
706C LEU* 4.1 17.9 - - + -
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Residues in contact with SER 438 (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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432C ASP* 3.0 29.2 + - - +
434C ASN* 3.3 7.3 + - - -
435C ASN* 2.5 39.4 + - - -
437C LEU* 1.3 74.0 - - - +
439C GLY* 1.3 61.1 + - - +
441C THR* 3.0 9.4 + - - -
442C HIS* 2.9 28.2 + - - +
604C ARG* 3.5 32.3 - - - +
1201C SRN 4.4 1.0 + - - -
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Residues in contact with GLY 439 (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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431C MET* 3.6 25.8 - - - -
432C ASP 3.0 13.2 + - - -
433C GLN* 4.7 0.9 - - - -
435C ASN 3.4 5.1 + - - -
436C PRO* 3.6 2.9 + - - -
437C LEU 3.3 0.4 - - - -
438C SER* 1.3 84.2 + - - +
440C LEU* 1.3 61.2 + - - +
442C HIS* 3.4 5.7 + - - +
443C LYS* 3.1 30.6 + - - +
629C ALA 6.1 0.2 - - - -
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Residues in contact with LEU 440 (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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44C LEU* 3.4 46.4 - - + +
45C LEU* 4.5 10.5 - - + -
436C PRO 3.2 14.4 + - - +
437C LEU* 3.0 14.2 + - + +
439C GLY* 1.3 77.0 - - - +
441C THR* 1.3 53.4 + - + +
443C LYS* 2.6 34.7 + - + +
444C ARG* 3.7 8.6 - - + +
580C VAL* 4.2 23.1 - - + -
625C ALA* 3.7 23.6 - - + +
628C ASP 4.3 4.0 - - - +
629C ALA* 4.3 16.7 + - + +
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Residues in contact with THR 441 (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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437C LEU* 2.9 31.8 + - + -
438C SER* 3.0 15.1 + - - -
440C LEU* 1.3 72.5 - - + +
442C HIS* 1.3 57.6 + - - +
443C LYS 2.6 18.2 - - - +
444C ARG* 4.6 3.0 - - - +
445C ARG* 3.2 32.3 + - - +
478C GLU* 3.9 18.6 - - - +
490C SER* 4.8 5.5 - - - -
579C SER* 6.1 0.4 - - - -
580C VAL* 5.1 7.2 - - + +
581C ALA* 3.9 11.2 - - + +
604C ARG* 3.3 17.4 + - - +
1201C SRN 3.9 1.8 - - - -
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Residues in contact with HIS 442 (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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165C VAL* 4.1 12.0 + - + +
167C VAL* 4.1 13.1 - - + +
429C GLN* 2.8 38.3 + - + +
430C PHE 3.0 27.4 - - - -
431C MET* 3.3 10.4 - - + +
432C ASP* 3.0 21.5 + - - +
438C SER 2.9 14.8 + - - +
439C GLY* 3.5 13.9 - - - +
440C LEU 3.3 0.2 - - - -
441C THR* 1.3 77.8 + - - +
443C LYS* 1.3 61.9 + - + +
445C ARG* 3.3 14.9 + - - +
1201C SRN 3.4 34.1 + - + +
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Residues in contact with LYS 443 (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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45C LEU* 3.4 33.0 - - + -
48C GLN* 3.9 19.3 - - + -
154C LYS* 3.1 16.6 + - - +
155C GLY 4.6 4.9 - - - +
156C THR* 3.1 30.9 - - - +
165C VAL* 3.9 17.7 - - + +
166C VAL 5.5 0.4 - - - -
167C VAL* 6.3 0.2 - - - +
431C MET* 3.3 24.0 - - - +
439C GLY 3.1 18.3 + - - +
440C LEU* 2.6 22.2 - - + +
441C THR 2.6 21.7 - - - +
442C HIS* 1.3 70.2 - - - +
444C ARG* 1.3 66.2 + - + +
445C ARG 3.0 5.6 - - - -
629C ALA 4.6 7.9 - - - -
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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