Contacts of the helix formed by residues 895 - 910 (chain D) in PDB entry 3H2V
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 895 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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894D ILE* 1.3 67.0 - - - +
896D GLN* 1.3 66.6 + - - +
897D PRO* 3.0 21.7 - - - +
898D MET* 2.9 40.0 + - + +
899D MET* 2.9 23.0 + - - +
934D SER* 3.3 28.1 + - - -
937D VAL* 3.5 22.3 - - + +
938D ARG* 4.1 8.5 - - - +
1020D THR* 4.4 7.8 - - - +
1024D VAL* 3.6 19.4 - - - +
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Residues in contact with GLN 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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896C GLN* 2.2 43.4 + - - +
894D ILE* 2.7 11.9 + - - +
895D ASN* 1.3 71.1 - - - +
897D PRO* 1.3 74.0 - - + +
899D MET* 3.7 4.7 - - - +
900D MET* 2.9 50.1 + - + +
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Residues in contact with PRO 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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895D ASN* 3.0 16.4 - - - +
896D GLN* 1.3 103.9 - - + +
898D MET* 1.3 59.0 + - - +
900D MET* 3.7 8.7 - - + +
901D ALA* 3.3 20.8 + - - +
1024D VAL* 3.6 23.6 - - + -
1028D GLN* 4.0 18.2 + - - +
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Residues in contact with MET 898 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
895D ASN* 2.9 32.1 - - + +
897D PRO* 1.3 74.4 - - - +
899D MET* 1.3 62.3 + - - +
900D MET 3.2 0.2 - - - -
901D ALA* 3.2 5.4 + - - +
902D ALA* 2.8 29.4 + - - +
930D MET* 3.6 38.7 - - - +
933D MET* 3.7 30.1 - - + -
934D SER* 3.4 21.1 - - - +
937D VAL* 4.7 11.4 - - - -
1023D LEU* 4.8 6.1 - - - -
1024D VAL* 3.8 23.6 - - + -
1027D ALA* 4.1 16.4 - - + -
1028D GLN* 6.1 0.2 - - - -
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Residues in contact with MET 899 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
885D PHE* 4.7 2.6 - - - -
894D ILE* 3.6 35.2 - - + -
895D ASN 2.9 11.4 + - - +
896D GLN* 3.7 4.3 - - - +
898D MET* 1.3 76.3 - - - +
900D MET* 1.3 59.7 + - - +
902D ALA* 3.6 4.6 - - - +
903D ARG* 2.9 41.6 + - - +
931D ALA* 3.3 39.9 - - + +
934D SER* 2.9 17.3 - - - +
935D ARG* 4.3 10.1 - - - +
92H TYR* 3.5 45.1 - - + +
93H LYS* 6.2 0.2 - - + -
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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
----------------------------------------------------------
896D GLN* 2.9 43.3 + - + +
897D PRO* 3.7 10.5 - - + +
899D MET* 1.3 77.4 - - - +
901D ALA* 1.3 59.2 - - - +
903D ARG* 3.4 30.5 + - - +
904D GLN* 2.9 48.4 + - + +
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Residues in contact with ALA 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 PRO 3.3 13.1 + - - +
898D MET* 3.2 6.4 + - - +
899D MET 3.2 0.2 - - - -
900D MET* 1.3 79.2 - - - +
902D ALA* 1.3 66.6 + - - +
904D GLN* 3.9 11.2 - - - +
905D LEU* 3.2 16.5 + - - +
930D MET* 5.3 0.7 - - + -
1027D ALA* 4.7 1.1 - - + -
1028D GLN* 4.0 24.9 - - + +
1031D MET* 3.6 32.5 - - + +
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Residues in contact with ALA 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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885D PHE* 4.5 5.6 - - + -
898D MET 2.8 18.3 + - - +
899D MET* 3.6 9.9 - - - +
901D ALA* 1.3 78.1 - - - +
903D ARG* 1.3 57.1 + - - +
905D LEU* 3.5 0.7 + - - +
906D HIS* 3.0 22.5 + - - +
927D ALA* 3.4 32.2 - - - +
930D MET* 3.6 20.1 - - + +
931D ALA* 3.8 12.6 - - + +
1031D MET* 4.1 3.8 - - - -
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Residues in contact with ARG 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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885D PHE* 3.7 35.8 - - + -
886D PRO 2.4 38.4 + - - -
887D GLU* 3.7 23.2 + - - +
899D MET* 2.9 29.9 + - - +
900D MET* 3.7 37.0 - - - +
902D ALA* 1.3 75.7 - - - +
904D GLN* 1.3 66.1 + - + +
906D HIS* 3.2 2.4 + - - +
907D ASP* 3.0 40.6 + - - +
92H TYR* 4.8 7.7 + - - -
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Residues in contact with GLN 904 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
900D MET* 2.9 38.6 + - + +
901D ALA* 3.4 10.0 + - - +
903D ARG* 1.3 76.9 - - + +
905D LEU* 1.3 62.0 + - - +
907D ASP* 3.7 8.5 + - - +
908D GLU* 3.5 17.8 + - - +
1031D MET* 6.1 0.7 - - + -
1032D GLN* 5.5 4.2 - - - +
1035D LYS* 4.2 28.4 + - + +
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Residues in contact with LEU 905 (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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901D ALA 3.2 10.6 + - - +
902D ALA 3.7 7.0 - - - +
903D ARG 3.2 0.2 - - - -
904D GLN* 1.3 74.6 - - - +
906D HIS* 1.3 66.7 + - - +
908D GLU* 2.9 16.2 + - + +
909D ALA* 3.2 10.8 + - + +
923D ALA* 3.2 38.8 - - + +
926D MET* 4.1 7.6 - - + -
927D ALA* 3.6 17.3 - - + +
1031D MET* 3.7 27.8 - - + +
1034D VAL* 4.0 12.8 - - + -
1035D LYS* 3.6 42.1 - - + +
1038D VAL* 5.4 1.8 - - + -
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Residues in contact with HIS 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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884D GLU 3.1 30.2 + - - -
885D PHE* 3.7 25.9 - + + +
902D ALA 3.0 12.1 + - - +
903D ARG* 3.4 12.6 - - - +
905D LEU* 1.3 79.9 - - - +
907D ASP* 1.3 58.7 + - - +
909D ALA* 3.4 4.1 + - - +
910D ARG* 3.0 55.2 + - + +
924D LYS* 4.5 27.6 - - + +
927D ALA* 3.8 16.7 - - + +
928D LEU* 5.1 8.5 - - + +
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Residues in contact with ASP 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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885D PHE* 5.3 4.3 - - - +
903D ARG* 3.0 39.4 + - - +
904D GLN* 4.0 8.4 - - - +
905D LEU 3.0 0.4 + - - -
906D HIS* 1.3 76.5 + - - +
908D GLU* 1.3 67.5 + - - +
910D ARG* 3.2 35.6 + - - +
911D LYS* 3.6 11.4 + - - +
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Residues in contact with GLU 908 (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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904D GLN 3.5 9.4 + - - +
905D LEU* 2.9 9.5 + - + +
907D ASP* 1.3 79.8 - - - +
909D ALA* 1.3 56.5 + - - +
911D LYS* 3.2 45.5 - - - +
912D TRP* 3.6 11.1 + - - +
1035D LYS* 4.2 26.3 + - + +
1038D VAL* 4.4 9.9 - - + +
1039D ARG* 3.1 52.9 + - + +
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Residues in contact with ALA 909 (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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905D LEU* 3.2 14.3 + - + +
906D HIS* 4.2 2.2 - - - +
908D GLU* 1.3 72.4 - - - +
910D ARG* 1.3 58.6 + - - +
911D LYS 2.9 9.4 + - - -
912D TRP 3.2 10.1 + - - +
920D ILE* 3.1 43.7 - - + +
923D ALA* 4.1 22.2 - - + -
924D LYS* 3.3 18.0 - - + +
1038D VAL* 5.3 4.5 - - + +
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Residues in contact with ARG 910 (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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884D GLU* 3.4 36.3 + - - +
906D HIS* 3.0 26.7 + - + +
907D ASP* 3.2 46.5 + - - +
909D ALA* 1.3 73.3 - - - +
911D LYS* 1.3 64.3 + - + +
912D TRP 3.1 3.5 + - - -
924D LYS* 4.0 12.3 - - - +
1061D LYS* 3.5 36.6 + - - +
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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