Contacts of the helix formed by residues 914 - 934 (chain H) in PDB entry 6X34
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 914 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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906H CYS* 5.4 7.2 - - + -
913H LEU* 1.3 80.7 - - - +
915H GLU* 1.3 65.4 + - - +
916H PRO* 3.2 11.9 - - + -
917H GLU* 3.6 4.0 + - + +
918H ARG* 3.3 20.1 + - - +
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Residues in contact with GLU 915 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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914H PRO* 1.3 75.9 - - - +
916H PRO* 1.3 58.4 - - - +
918H ARG* 3.8 6.3 - - - +
919H ASN* 2.9 30.8 + - - +
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Residues in contact with PRO 916 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
914H PRO* 3.2 8.1 - - + -
915H GLU* 1.3 78.0 - - - +
917H GLU* 1.3 58.7 + - - +
919H ASN* 3.3 6.0 + - + +
920H TYR* 2.9 29.3 + - - +
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Residues in contact with GLU 917 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
882H TRP* 5.0 8.3 - - + -
906H CYS* 4.2 25.3 - - + +
908H VAL 5.0 2.7 - - - +
910H PHE* 4.6 3.7 - - + +
913H LEU* 3.7 27.8 - - + -
914H PRO* 3.6 3.5 + - + +
916H PRO* 1.3 78.0 - - - +
918H ARG* 1.3 57.5 + - - +
920H TYR* 3.3 10.4 + - - +
921H ASN* 2.9 29.8 + - - +
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Residues in contact with ARG 918 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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910H PHE* 4.0 32.0 - - + +
914H PRO 3.3 15.8 + - - +
915H GLU* 3.8 7.0 - - - +
916H PRO 3.3 0.6 - - - -
917H GLU* 1.3 79.8 - - - +
919H ASN* 1.3 55.9 + - - +
921H ASN* 3.3 2.6 + - - +
922H LEU* 2.9 39.5 + - + +
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Residues in contact with ASN 919 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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915H GLU 2.9 18.3 + - - +
916H PRO* 3.7 5.8 - - + +
918H ARG* 1.3 75.9 - - - +
920H TYR* 1.3 58.6 + - - +
922H LEU* 3.3 9.7 + - - +
923H GLN* 2.9 29.6 + - - +
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Residues in contact with TYR 920 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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878H ILE* 6.3 4.0 - - + -
882H TRP* 4.2 40.7 - + + -
916H PRO 2.9 18.6 + - - +
917H GLU* 3.7 7.0 - - - +
919H ASN* 1.3 77.1 - - - +
921H ASN* 1.3 62.1 + - + +
923H GLN* 3.3 7.7 + - + +
924H MET* 2.9 39.7 + - + +
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Residues in contact with ASN 921 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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875H ALA* 3.5 28.8 - - + +
878H ILE* 5.8 2.7 - - + -
879H HIS* 5.2 5.8 - - + +
910H PHE* 4.2 19.1 - - + -
917H GLU 2.9 17.6 + - - +
918H ARG 3.7 3.4 - - - +
920H TYR* 1.3 83.4 - - + +
922H LEU* 1.3 57.8 + - + +
924H MET* 3.3 6.1 + - - +
925H SER* 2.9 30.3 + - - -
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Residues in contact with LEU 922 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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871H ARG* 5.9 2.5 - - + +
872H GLU* 6.1 3.4 - - - -
875H ALA* 5.0 9.6 - - + -
910H PHE* 5.7 9.9 - - + -
918H ARG* 2.9 27.9 + - + +
919H ASN* 3.7 7.6 - - - +
921H ASN* 1.3 77.1 - - + +
923H GLN* 1.3 57.6 + - - +
925H SER* 3.3 6.6 + - - -
926H GLY* 2.9 25.5 + - - -
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Residues in contact with GLN 923 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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919H ASN 2.9 17.6 + - - +
920H TYR* 3.7 8.7 - - + +
922H LEU* 1.3 77.3 - - - +
924H MET* 1.3 57.5 + - - +
926H GLY* 3.3 2.1 + - - +
927H GLU* 2.9 29.8 + - - +
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Residues in contact with MET 924 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
878H ILE* 4.9 15.7 - - + -
920H TYR* 2.9 31.7 + - + +
921H ASN* 3.7 7.4 - - - +
922H LEU 3.3 0.2 - - - -
923H GLN* 1.3 76.1 - - - +
925H SER* 1.3 58.5 + - - +
927H GLU* 3.3 6.7 + - - +
928H THR* 2.9 34.8 + - - +
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Residues in contact with SER 925 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
871H ARG* 3.2 40.7 - - - +
874H LEU* 4.3 6.8 - - - +
875H ALA* 3.7 13.4 - - - +
878H ILE* 6.0 0.2 - - - +
921H ASN 2.9 17.9 + - - -
922H LEU* 3.7 7.6 - - - -
923H GLN 3.3 0.2 - - - -
924H MET* 1.3 78.0 - - - +
926H GLY* 1.3 56.1 + - - +
928H THR* 3.3 6.2 + - - -
929H LEU* 2.9 30.0 + - - +
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Residues in contact with GLY 926 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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871H ARG* 5.1 2.4 - - - +
922H LEU 2.9 16.1 + - - -
923H GLN* 3.8 2.5 - - - -
925H SER* 1.3 77.2 - - - +
927H GLU* 1.3 56.8 + - - +
929H LEU* 3.3 6.2 + - - +
930H LYS* 2.9 29.8 + - - +
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Residues in contact with GLU 927 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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923H GLN 2.9 17.6 + - - +
924H MET* 3.7 7.0 - - - +
925H SER 3.3 0.2 - - - -
926H GLY* 1.3 75.5 - - - +
928H THR* 1.3 58.3 + - - +
930H LYS* 3.3 6.1 + - - +
931H THR* 2.9 30.2 + - - -
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Residues in contact with THR 928 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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874H LEU* 4.9 7.4 - - + +
924H MET* 2.9 18.6 + - - +
925H SER* 3.7 7.0 - - - -
927H GLU* 1.3 77.4 - - - +
929H LEU* 1.3 57.5 + - - +
931H THR* 3.3 6.4 + - - -
932H LEU* 2.9 30.4 + - + +
1039H LEU 5.8 0.4 - - - +
1042H ALA* 4.9 11.0 - - + +
1043H VAL* 4.6 25.6 - - + +
1046H LEU* 4.8 13.9 - - + -
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Residues in contact with LEU 929 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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867H LEU* 5.2 10.8 - - + +
871H ARG* 4.9 13.0 - - + +
925H SER 2.9 17.8 + - - +
926H GLY* 3.7 7.2 - - - +
928H THR* 1.3 77.3 - - - +
930H LYS* 1.3 57.5 + - - +
932H LEU* 3.3 6.5 + - - +
933H LEU* 2.9 30.9 + - - +
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Residues in contact with LYS 930 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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926H GLY 2.9 18.2 + - - +
927H GLU* 3.7 6.3 - - - +
929H LEU* 1.3 76.6 - - - +
931H THR* 1.3 57.3 + - - +
933H LEU* 3.3 5.9 + - - +
934H ALA* 2.9 30.7 + - - +
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Residues in contact with THR 931 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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927H GLU 2.9 17.4 + - - -
928H THR* 3.7 6.7 - - - -
930H LYS* 1.3 74.6 - - - +
932H LEU* 1.3 61.8 + - - +
934H ALA* 3.6 16.1 + - - +
935H LEU* 3.8 6.6 + - - +
988H LEU* 3.7 34.0 - - - +
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Residues in contact with LEU 932 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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928H THR* 2.9 19.9 + - + +
929H LEU* 3.7 7.2 - - - +
931H THR* 1.3 78.0 - - - +
933H LEU* 1.3 60.5 + - - +
935H LEU* 3.4 18.9 + - - +
936H GLY 4.3 1.2 + - - -
937H CYS* 5.3 1.2 + - - +
1043H VAL* 6.0 5.2 - - + -
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Residues in contact with LEU 933 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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929H LEU 2.9 17.7 + - - +
930H LYS* 3.9 5.6 - - - +
932H LEU* 1.3 72.7 - - - +
934H ALA* 1.3 64.3 + - - +
935H LEU 3.1 3.6 + - - -
936H GLY* 3.3 13.6 + - - +
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Residues in contact with ALA 934 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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930H LYS 2.9 17.2 + - - +
931H THR* 3.8 10.3 - - - +
932H LEU 3.3 0.6 - - - -
933H LEU* 1.3 76.8 - - - +
935H LEU* 1.3 61.9 + - - +
936H GLY* 3.5 0.6 + - - -
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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
------------------------------------------------------------
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