Contacts of the helix formed by residues 850 - 861 (chain A) in PDB entry 4P5Q
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 850 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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720A VAL* 3.9 30.5 - - + -
818A MET* 4.0 15.0 - - + -
848A ASP 3.4 8.5 - - - +
849A CYS* 1.3 92.3 - - - +
851A ALA* 1.3 64.5 + - - +
852A ALA* 4.3 4.7 - - + +
853A LEU* 3.0 18.3 + - + +
854A TYR* 3.1 10.7 + - - +
888A LEU* 3.7 38.8 - - + +
890A ILE 3.4 9.2 - - - +
891A ILE* 3.8 5.6 - - + -
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Residues in contact with ALA 851 (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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849A CYS 3.5 1.8 + - - -
850A PRO* 1.3 70.8 - - - +
852A ALA* 1.3 62.5 + - - +
854A TYR* 3.3 0.9 + - - +
855A GLN* 2.9 26.0 + - - +
890A ILE* 2.8 38.5 + - + +
891A ILE 4.6 0.2 - - - -
892A THR* 3.7 24.6 - - + +
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Residues in contact with ALA 852 (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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850A PRO* 3.2 1.7 - - + +
851A ALA* 1.3 79.7 - - - +
853A LEU* 1.3 57.9 + - - +
855A GLN* 3.6 5.7 + - - +
856A LEU* 3.1 25.6 + - - +
877A ILE* 5.7 1.7 - - - +
881A LEU* 4.0 33.1 - - + +
887A SER* 5.4 7.2 - - - +
888A LEU* 4.9 7.6 - - + -
890A ILE 4.7 0.6 + - - -
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Residues in contact with LEU 853 (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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720A VAL* 4.3 2.0 - - + -
724A VAL* 3.9 22.0 - - + -
727A LEU* 4.9 1.8 - - + -
814A LEU* 3.7 21.7 - - + +
818A MET* 3.8 31.9 - - + -
849A CYS* 4.0 9.2 - - - -
850A PRO* 3.0 26.4 + - + +
852A ALA* 1.3 75.5 - - - +
854A TYR* 1.3 66.4 + - - +
856A LEU* 3.2 9.6 + - + +
857A MET* 3.1 27.6 + - + +
878A LEU* 4.0 18.6 - - + -
881A LEU* 3.8 24.7 - - + -
888A LEU* 4.3 1.1 - - + -
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Residues in contact with TYR 854 (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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842A ARG* 4.7 1.4 - - - +
843A LEU 2.6 29.4 + - - -
844A PRO* 3.6 3.4 - - - +
845A PRO* 3.4 41.8 - - + +
846A PRO* 4.4 0.4 - - + -
849A CYS* 3.9 7.2 - - - -
850A PRO 3.1 9.7 + - - +
851A ALA 4.0 1.6 - - - +
853A LEU* 1.3 76.3 - - - +
855A GLN* 1.3 63.6 + - - +
857A MET* 3.1 26.9 + - - +
858A LEU* 3.0 55.0 + - + +
861A TRP* 4.5 3.1 - + - -
892A THR* 4.0 30.5 - - + +
902A LEU* 4.0 14.5 - - + +
904A ASP 5.0 2.3 - - - -
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Residues in contact with GLN 855 (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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851A ALA 2.9 18.7 + - - +
852A ALA* 3.8 6.1 - - - +
854A TYR* 1.3 77.8 - - - +
856A LEU* 1.3 55.4 + - - +
858A LEU* 3.2 23.8 + - - +
859A ASP* 2.9 64.5 + - - +
862A GLN* 5.6 1.0 - - - +
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Residues in contact with LEU 856 (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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810A TYR* 4.8 1.6 - - + -
814A LEU* 3.7 19.7 - - + -
852A ALA 3.1 16.0 + - - +
853A LEU* 3.5 13.2 - - + +
855A GLN* 1.3 77.0 - - - +
857A MET* 1.3 63.2 + - - +
859A ASP* 3.2 10.7 + - + +
860A CYS* 2.9 39.3 + - - -
869A PRO* 4.6 6.3 - - + -
874A ILE* 4.3 23.3 - - + -
877A ILE* 3.9 37.9 - - + -
878A LEU* 4.0 26.7 - - + -
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Residues in contact with MET 857 (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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811A GLY* 4.0 6.7 - - - +
814A LEU* 3.5 44.4 - - + +
815A TRP* 3.8 29.6 - - - -
818A MET* 3.9 7.4 - - + -
846A PRO* 4.1 4.7 - - + -
849A CYS* 3.8 28.5 - - - -
853A LEU 3.1 12.2 + - - +
854A TYR* 3.1 23.3 + - + +
856A LEU* 1.3 75.2 - - - +
858A LEU* 1.3 62.6 + - - +
860A CYS* 3.1 7.8 + - - +
861A TRP* 3.0 48.1 + - + -
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Residues in contact with LEU 858 (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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842A ARG* 4.2 10.3 + - + -
854A TYR* 3.0 55.8 + - + +
855A GLN* 3.2 28.2 + - - +
857A MET* 1.3 76.2 - - - +
859A ASP* 1.3 60.4 + - - +
861A TRP* 3.1 29.1 + - + +
862A GLN* 3.0 23.5 + - - +
904A ASP* 3.8 39.0 - - - +
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Residues in contact with ASP 859 (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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855A GLN* 2.9 48.5 + - - +
856A LEU* 3.5 14.5 - - + +
858A LEU* 1.3 78.0 - - - +
860A CYS* 1.3 61.1 + - - +
862A GLN* 3.3 29.9 + - - +
867A ASN 4.4 1.5 - - - +
868A ARG* 3.6 3.5 - - - +
869A PRO* 3.5 27.9 - - + +
877A ILE* 5.7 3.1 - - - +
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Residues in contact with CYS 860 (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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807A VAL* 3.5 39.5 - - - +
808A TRP* 3.4 12.8 - - - -
810A TYR* 4.2 5.6 - - - -
811A GLY* 3.6 22.0 - - - -
814A LEU* 5.3 0.2 - - - -
856A LEU* 2.9 24.8 + - - +
857A MET 3.5 7.9 - - - +
859A ASP* 1.3 76.0 - - - +
861A TRP* 1.3 59.9 + - - +
862A GLN 3.4 0.9 - - - -
868A ARG* 3.2 21.9 + - - -
869A PRO* 4.2 6.1 - - - -
874A ILE* 4.0 17.7 - - - -
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Residues in contact with TRP 861 (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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808A TRP* 3.2 37.4 + + + -
811A GLY* 3.3 23.6 - - - -
812A ILE* 3.3 41.1 - - + +
815A TRP* 4.1 6.3 - + + -
825A TYR* 5.5 1.3 - - - -
842A ARG* 2.9 53.4 + - + +
843A LEU* 3.8 41.1 - - + -
854A TYR* 4.5 2.0 - + - -
857A MET* 3.0 44.5 + - + +
858A LEU* 3.1 16.6 + - + +
859A ASP 3.1 0.8 - - - -
860A CYS* 1.3 83.1 - - - +
862A GLN* 1.3 65.6 + - - +
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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