Contacts of the helix formed by residues 834 - 840 (chain D) 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 PRO 834 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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824D PRO* 4.0 2.5 - - + -
831D VAL* 4.6 10.5 - - + -
832D LYS 4.4 3.6 - - - +
833D GLU* 1.3 92.3 - - + +
835D LEU* 1.3 61.7 + - - +
836D ARG* 3.2 12.1 - - + +
837D ASP* 3.5 26.7 + - + +
838D ARG* 3.0 26.5 + - - +
873D GLU* 5.0 4.5 - - - +
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Residues in contact with LEU 835 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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822D MET* 4.1 15.3 - - + +
823D THR 4.5 2.0 - - - -
824D PRO* 3.6 37.7 - - + +
834D PRO* 1.3 73.4 - - - +
836D ARG* 1.3 57.2 + - - +
838D ARG* 4.2 5.8 - - + -
839D VAL* 2.9 50.8 + - + +
869D CYS* 5.2 0.4 - - - -
872D LEU* 4.0 26.7 - - + +
873D GLU* 5.3 7.3 + - + -
877D VAL* 3.4 30.7 - - + +
878D ASP 4.4 4.9 - - - +
880D VAL* 4.9 6.3 - - + +
990D ARG* 4.9 7.9 - - - +
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Residues in contact with ARG 836 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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834D PRO* 3.2 6.6 - - + +
835D LEU* 1.3 77.2 - - - +
837D ASP* 1.3 67.8 + - - +
840D LEU* 3.0 46.9 + - + +
866D GLU* 3.4 37.3 + - - +
869D CYS* 2.8 45.4 + - - +
870D ASP* 3.0 29.1 + - - -
873D GLU* 3.4 28.5 + - - +
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Residues in contact with ASP 837 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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497D GLU* 4.7 10.3 - - - +
833D GLU* 4.8 10.3 - - + +
834D PRO* 3.5 29.9 + - + +
835D LEU 3.5 0.4 - - - -
836D ARG* 1.3 87.4 - - - +
838D ARG* 1.3 62.9 + - - +
840D LEU* 4.7 5.4 + - - +
1247D LYS* 5.5 6.2 + - - -
1249D ASN* 4.7 7.8 - - - +
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Residues in contact with ARG 838 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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822D MET* 3.0 54.2 - - + +
823D THR* 3.8 21.6 + - - +
824D PRO* 4.3 4.7 - - + -
825D VAL* 3.7 29.9 - - - +
833D GLU* 3.7 23.6 - - + -
834D PRO 3.0 20.0 + - - +
835D LEU* 3.8 12.3 - - + +
836D ARG 3.1 0.2 - - - -
837D ASP* 1.3 81.3 - - - +
839D VAL* 1.3 60.5 + - - +
840D LEU 3.6 1.3 + - - +
842D ARG* 4.5 7.4 + - - -
1231D ARG* 5.7 5.3 - - - +
1234D VAL* 5.6 3.6 - - - +
1235D ASN* 3.9 20.2 + - - +
1242D ARG* 5.1 4.4 - - - +
1249D ASN* 4.7 7.4 - - - +
1250D ASP* 3.6 27.2 + - - +
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Residues in contact with VAL 839 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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822D MET* 4.4 12.3 - - + -
835D LEU* 2.9 42.5 + - + +
836D ARG* 4.6 2.0 - - - +
838D ARG* 1.3 73.5 - - + +
840D LEU* 1.3 67.1 + - - +
841D GLY 3.2 4.0 + - - -
842D ARG* 3.3 18.5 + - + +
864D LEU* 3.4 24.0 - - + +
869D CYS* 5.2 3.6 - - - -
872D LEU* 4.7 13.7 - - + -
880D VAL* 4.5 14.8 - - + -
882D VAL* 3.7 29.8 - - + -
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Residues in contact with LEU 840 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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610D ARG* 6.0 3.1 - - - +
836D ARG* 3.0 31.4 + - + +
837D ASP* 4.7 4.9 - - - +
838D ARG 3.6 2.6 - - - +
839D VAL* 1.3 79.1 - - - +
841D GLY* 1.3 58.8 + - - +
842D ARG* 3.6 2.5 + - - +
864D LEU* 3.3 24.9 - - - +
865D HIS 3.8 16.8 - - - +
866D GLU* 3.8 22.7 - - + +
869D CYS* 4.2 14.1 - - + -
901D ARG* 3.9 15.9 - - - +
903D LEU* 5.7 1.6 - - - +
1249D ASN* 4.6 14.9 + - - +
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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