Contacts of the helix formed by residues 892 - 907 (chain D) in PDB entry 6AH0
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 GLN 892 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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620D LEU 4.5 5.5 + - - -
621D HIS 5.7 1.4 + - - -
622D ASP 5.1 7.9 + - - -
623D ASP* 6.0 4.3 - - - +
625D GLY 5.7 0.2 - - - -
626D PRO* 5.3 8.8 - - - -
890D GLU 3.9 2.6 + - - -
891D SER* 1.3 71.2 - - - +
893D MET* 1.3 63.9 + - - +
894D VAL 3.1 4.8 + - - -
895D SER* 3.1 14.9 + - - -
896D LYS 4.1 1.7 + - - -
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Residues in contact with MET 893 (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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626D PRO* 4.7 17.6 - - - +
891D SER* 3.1 6.2 - - - +
892D GLN* 1.3 76.7 - - - +
894D VAL* 1.3 62.6 + - - +
896D LYS* 3.1 5.0 + - - +
897D LEU* 2.9 22.0 + - - -
925D LEU* 6.4 2.0 - - - +
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Residues in contact with VAL 894 (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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891D SER 4.8 1.8 + - - -
892D GLN 3.1 2.0 + - - -
893D MET* 1.3 76.3 - - - +
895D SER* 1.3 62.8 + - - +
896D LYS 3.4 0.3 + - - -
897D LEU* 3.4 10.5 + - - +
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Residues in contact with SER 895 (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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892D GLN 3.1 10.3 + - - -
894D VAL* 1.3 77.1 - - - +
896D LYS* 1.3 58.8 + - - +
898D PRO 5.0 1.6 - - - -
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Residues in contact with LYS 896 (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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892D GLN 4.1 2.4 + - - -
893D MET 3.1 7.7 + - - -
895D SER* 1.3 75.0 - - - +
897D LEU* 1.3 54.2 + - - +
898D PRO 3.2 2.5 - - - -
899D ASP* 2.7 30.1 + - - -
900D MET* 3.1 9.6 + - - -
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Residues in contact with LEU 897 (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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893D MET 2.9 14.6 + - - -
894D VAL* 3.4 11.0 + - - +
895D SER 3.4 0.2 - - - -
896D LYS* 1.3 74.7 - - - +
898D PRO* 1.3 60.8 - - - +
900D MET* 3.5 2.6 + - - +
901D LEU* 3.1 20.3 + - - -
960D ALA* 5.4 2.8 - - - -
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Residues in contact with PRO 898 (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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894D VAL 5.1 0.6 - - - -
895D SER 5.0 1.6 - - - -
896D LYS 3.0 3.8 - - - -
897D LEU* 1.3 74.1 - - - +
899D ASP* 1.3 61.3 + - - +
901D LEU* 3.6 1.3 + - - -
902D ASN* 3.3 18.0 + - - -
960D ALA* 4.3 26.2 - - - +
964D LEU* 6.1 1.0 - - - -
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Residues in contact with ASP 899 (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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896D LYS 2.7 14.6 + - - -
898D PRO* 1.3 70.3 - - - +
900D MET* 1.3 61.7 + - - +
902D ASN* 3.5 2.4 + - - +
903D ALA* 3.4 17.8 + - - -
994D THR* 6.4 2.0 - - - +
995D ASN 6.0 4.0 - - - +
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Residues in contact with MET 900 (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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896D LYS 3.1 12.6 + - - -
897D LEU* 4.0 2.9 - - - +
898D PRO 3.4 0.2 - - - -
899D ASP* 1.3 75.9 - - - +
901D LEU* 1.3 65.7 + - - +
903D ALA* 3.6 1.6 + - - +
904D GLU* 3.4 15.4 + - - -
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Residues in contact with LEU 901 (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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897D LEU 3.1 16.1 + - - -
898D PRO* 4.1 1.3 - - - -
900D MET* 1.3 74.3 - - - +
902D ASN* 1.3 68.3 + - - +
904D GLU* 3.0 10.9 + - - -
905D ILE* 3.0 9.2 + - - -
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Residues in contact with ASN 902 (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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898D PRO 3.3 13.6 + - - -
899D ASP 3.5 3.6 + - - -
900D MET 3.4 0.2 - - - -
901D LEU* 1.3 73.1 - - - +
903D ALA* 1.3 49.1 + - - +
905D ILE* 2.7 25.7 + - - +
906D VAL* 2.8 15.3 + - - -
985D GLY 6.0 1.8 - - - -
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Residues in contact with ALA 903 (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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598D ARG* 5.7 5.5 - - - +
899D ASP 3.4 13.4 + - - -
900D MET 3.6 2.7 + - - -
901D LEU 3.4 0.2 - - - -
902D ASN* 1.3 74.0 - - - +
904D GLU* 1.3 56.5 + - - +
906D VAL* 3.5 4.2 + - - +
907D LEU* 3.1 21.0 + - - -
989D SER* 5.0 17.2 - - - +
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Residues in contact with GLU 904 (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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900D MET 3.4 9.3 + - - -
901D LEU* 3.0 8.6 + - - +
903D ALA* 1.3 74.7 - - - +
905D ILE* 1.3 63.3 + - - +
907D LEU* 3.5 1.9 + - - +
908D GLY 3.2 2.1 + - - -
909D ASN* 2.9 30.1 + - - +
910D VAL* 3.3 7.6 + - - +
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Residues in contact with ILE 905 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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901D LEU 3.0 7.9 + - - -
902D ASN* 2.7 11.5 + - - +
904D GLU* 1.3 70.3 - - - +
906D VAL* 1.3 61.8 + - - +
908D GLY* 3.0 18.5 + - - -
910D VAL* 3.8 19.1 - - - +
981D VAL* 5.7 6.3 + - - -
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Residues in contact with VAL 906 (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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598D ARG 5.9 2.2 - - - -
902D ASN 2.8 13.1 + - - -
903D ALA* 3.5 5.6 + - - +
904D GLU 3.2 0.2 - - - -
905D ILE* 1.3 77.5 - - - +
907D LEU* 1.3 58.2 + - - +
908D GLY* 3.5 0.3 + - - -
985D GLY 6.2 1.3 - - - -
986D ARG* 5.7 10.3 - - - +
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Residues in contact with LEU 907 (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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598D ARG* 5.8 4.2 + - - +
903D ALA 3.1 15.2 + - - -
904D GLU* 3.5 2.4 + - - +
905D ILE 3.2 0.4 - - - -
906D VAL* 1.3 76.0 - - - +
908D GLY* 1.3 61.6 + - - +
909D ASN* 3.2 3.7 + - - +
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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