Contacts of the helix formed by residues 801 - 810 (chain A) in PDB entry 3F2B
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 801 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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340A GLU* 3.9 24.0 - - + +
341A LYS 3.8 20.9 - - - +
342A ARG 4.4 0.2 - - - +
781A THR* 4.5 5.2 - - - +
785A LEU* 4.6 7.6 - - + -
797A LYS* 3.1 32.4 + - + +
799A ILE 3.6 0.2 - - - -
800A VAL* 1.3 91.3 - - + +
802A ASP* 1.3 72.7 + - - +
803A ASN 3.4 0.7 - - - -
804A THR* 3.6 3.0 - - - +
805A GLN* 2.7 46.1 + - - +
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Residues in contact with ASP 802 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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797A LYS* 3.3 38.1 + - - +
798A GLU* 3.3 29.1 + - + +
801A VAL* 1.3 81.2 - - - +
803A ASN* 1.3 63.4 + - - +
805A GLN* 3.5 7.7 + - - +
806A LYS* 2.8 28.4 + - - +
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Residues in contact with ASN 803 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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737A PRO* 4.4 18.5 - - + +
738A VAL 3.5 30.1 + - - +
739A VAL* 3.8 8.1 - - + -
798A GLU* 2.8 49.2 + - - +
799A ILE* 4.1 2.5 - - - +
802A ASP* 1.3 76.1 - - - +
804A THR* 1.3 60.6 + - - +
806A LYS* 3.6 11.7 - - - +
807A ILE* 2.9 35.5 + - - +
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Residues in contact with THR 804 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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342A ARG 3.7 1.8 - - - -
343A VAL* 2.7 56.3 + - + +
345A LEU* 3.7 14.9 - - - +
739A VAL* 3.8 10.5 - - - +
740A ALA 4.1 11.6 + - - -
799A ILE 4.5 3.7 + - - -
800A VAL 3.0 27.3 + - - +
801A VAL* 3.6 6.2 + - - +
803A ASN* 1.3 77.7 - - - +
805A GLN* 1.3 66.6 + - + +
807A ILE* 3.5 4.2 + - - +
808A ALA* 3.3 19.8 + - - +
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Residues in contact with GLN 805 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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339A GLY 3.4 23.9 + - - +
341A LYS 2.8 27.7 + - - +
343A VAL* 4.4 6.5 - - + -
373A PRO* 4.2 19.5 - - + +
801A VAL* 2.7 24.2 + - - +
802A ASP* 3.5 6.9 + - - +
804A THR* 1.3 80.6 - - - +
806A LYS* 1.3 64.3 + - - +
808A ALA* 3.4 4.7 + - + +
809A SER* 3.1 23.4 + - - +
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Residues in contact with LYS 806 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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737A PRO* 5.6 7.6 - - + -
802A ASP 2.8 21.5 + - - +
803A ASN* 3.2 17.1 + - - +
805A GLN* 1.3 70.5 - - - +
807A ILE* 1.3 69.2 + - + +
809A SER* 3.0 28.0 + - - -
810A LEU* 3.3 24.5 + - + +
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Residues in contact with ILE 807 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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345A LEU* 4.1 16.2 - - + -
624A LEU* 3.9 27.1 - - + -
665A LEU* 4.3 10.5 - - + -
695A ASP* 4.5 4.9 - - + +
696A PHE* 4.0 28.3 - - + -
737A PRO* 4.5 17.3 - - + -
739A VAL* 4.2 16.2 - - + -
803A ASN 2.9 20.1 + - - +
804A THR 3.8 4.5 - - - +
806A LYS* 1.3 75.0 - - + +
808A ALA* 1.3 59.3 + - - +
810A LEU* 2.9 41.1 + - + +
811A ILE* 3.5 9.4 - - + +
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Residues in contact with ALA 808 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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343A VAL* 3.9 21.8 - - + -
345A LEU* 5.0 0.2 - - - +
373A PRO* 5.8 1.6 - - + -
374A ALA* 4.2 8.7 - - + -
399A LYS* 2.5 31.1 + - - +
401A ILE* 4.0 23.8 - - + -
804A THR 3.3 11.3 + - - +
805A GLN* 3.5 9.9 - - + +
806A LYS 3.2 0.2 - - - -
807A ILE* 1.3 80.0 - - - +
809A SER* 1.3 57.2 + - - +
811A ILE* 3.2 7.8 + - - +
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Residues in contact with SER 809 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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399A LYS* 4.5 2.7 - - - +
805A GLN 3.1 13.3 + - - -
806A LYS* 3.0 23.2 + - - -
808A ALA* 1.3 74.4 - - - +
810A LEU* 1.3 61.9 + - - +
811A ILE 3.2 7.8 + - - +
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Residues in contact with LEU 810 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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626A GLN* 3.1 29.2 + - - +
665A LEU* 3.8 26.9 - - + -
806A LYS* 3.6 28.0 - - + +
807A ILE* 2.9 24.9 + - + +
809A SER* 1.3 81.2 - - - +
811A ILE* 1.3 60.8 + - - +
812A GLY 4.0 0.7 + - - -
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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