Contacts of the helix formed by residues 914 - 934 (chain F) 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 F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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906F CYS* 5.4 7.6 - - + -
913F LEU* 1.3 80.8 - - - +
915F GLU* 1.3 65.6 + - - +
916F PRO* 3.2 11.0 - - + -
917F GLU* 3.6 3.9 + - + +
918F ARG* 3.3 20.7 + - - +
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Residues in contact with GLU 915 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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914F PRO* 1.3 75.6 - - - +
916F PRO* 1.3 58.9 - - - +
918F ARG* 3.8 6.3 - - - +
919F ASN* 2.9 31.5 + - - +
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Residues in contact with PRO 916 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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914F PRO* 3.2 7.9 - - + -
915F GLU* 1.3 77.9 - - - +
917F GLU* 1.3 59.4 + - - +
919F ASN* 3.3 5.7 + - + +
920F TYR* 2.9 29.1 + - - +
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Residues in contact with GLU 917 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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882F TRP* 5.0 8.7 - - + -
906F CYS* 4.2 24.8 - - + +
908F VAL 5.0 1.8 - - - +
910F PHE* 4.6 5.2 - - - +
913F LEU* 3.7 27.8 - - + -
914F PRO* 3.6 3.3 + - - +
915F GLU 3.5 0.2 - - - -
916F PRO* 1.3 79.9 - - - +
918F ARG* 1.3 57.8 + - - +
920F TYR* 3.3 10.0 + - - +
921F ASN* 2.9 30.0 + - - +
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Residues in contact with ARG 918 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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910F PHE* 4.0 33.8 - - + +
914F PRO 3.3 15.3 + - - +
915F GLU* 3.8 7.0 - - - +
916F PRO 3.3 0.4 - - - -
917F GLU* 1.3 79.0 - - - +
919F ASN* 1.3 57.2 + - - +
921F ASN* 3.3 2.3 + - - +
922F LEU* 2.9 39.4 + - + +
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Residues in contact with ASN 919 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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915F GLU 2.9 18.3 + - - +
916F PRO* 3.7 5.8 - - + +
918F ARG* 1.3 76.3 - - - +
920F TYR* 1.3 57.9 + - - +
922F LEU* 3.3 9.7 + - - +
923F GLN* 2.9 30.3 + - - +
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Residues in contact with TYR 920 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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878F ILE* 6.3 3.8 - - + -
882F TRP* 4.2 39.4 - + + -
916F PRO 2.9 18.2 + - - +
917F GLU* 3.7 7.0 - - - +
919F ASN* 1.3 76.8 - - - +
921F ASN* 1.3 62.2 + - + +
923F GLN* 3.3 6.5 + - + +
924F MET* 2.9 38.2 + - + +
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Residues in contact with ASN 921 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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875F ALA* 3.5 29.1 - - + +
878F ILE* 5.8 2.5 - - + -
879F HIS* 5.2 5.8 - - + +
910F PHE* 4.2 18.8 - - + -
917F GLU 2.9 17.4 + - - +
918F ARG 3.7 3.8 - - - +
920F TYR* 1.3 82.3 - - + +
922F LEU* 1.3 58.9 + - + +
924F MET* 3.3 5.4 + - - +
925F SER* 2.9 29.8 + - - -
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Residues in contact with LEU 922 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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871F ARG* 5.9 1.8 - - + +
872F GLU* 6.1 3.6 - - - -
875F ALA* 5.0 9.9 - - + -
910F PHE* 5.7 9.4 - - + -
918F ARG* 2.9 26.2 + - + +
919F ASN* 3.7 8.1 - - - +
921F ASN* 1.3 76.4 - - - +
923F GLN* 1.3 58.3 + - - +
925F SER* 3.3 5.7 + - - -
926F GLY* 2.9 25.6 + - - -
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Residues in contact with GLN 923 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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919F ASN 2.9 17.4 + - - +
920F TYR* 3.7 8.1 - - + +
922F LEU* 1.3 77.7 - - - +
924F MET* 1.3 56.6 + - - +
926F GLY* 3.3 1.6 + - - -
927F GLU* 2.9 30.4 + - - +
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Residues in contact with MET 924 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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878F ILE* 4.9 16.2 - - + -
920F TYR* 2.9 32.8 + - + +
921F ASN* 3.7 7.2 - - - +
923F GLN* 1.3 75.4 - - - +
925F SER* 1.3 58.4 + - - +
927F GLU* 3.3 7.0 + - - +
928F THR* 2.9 34.6 + - - +
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Residues in contact with SER 925 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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871F ARG* 3.2 40.5 - - - +
874F LEU* 4.3 6.3 - - - +
875F ALA* 3.7 13.8 - - - +
878F ILE* 6.0 0.2 - - - +
921F ASN 2.9 17.4 + - - -
922F LEU* 3.7 7.9 - - - -
924F MET* 1.3 78.3 - - - +
926F GLY* 1.3 56.6 + - - +
928F THR* 3.3 5.9 + - - -
929F LEU* 2.9 30.1 + - - +
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Residues in contact with GLY 926 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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871F ARG* 5.1 2.9 - - - +
922F LEU 2.9 15.7 + - - -
923F GLN* 3.8 3.1 - - - -
925F SER* 1.3 76.8 - - - +
927F GLU* 1.3 55.9 + - - +
929F LEU* 3.3 6.2 + - - +
930F LYS* 2.9 30.2 + - - +
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Residues in contact with GLU 927 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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923F GLN 2.9 18.0 + - - +
924F MET* 3.7 7.0 - - - +
926F GLY* 1.3 75.5 - - - +
928F THR* 1.3 58.2 + - - +
930F LYS* 3.3 6.1 + - - +
931F THR* 2.9 30.0 + - - -
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Residues in contact with THR 928 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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874F LEU* 4.9 8.0 - - + +
924F MET* 2.9 19.5 + - - +
925F SER* 3.7 6.5 - - - -
927F GLU* 1.3 75.4 - - - +
929F LEU* 1.3 58.3 + - - +
931F THR* 3.3 7.1 + - - -
932F LEU* 2.9 31.0 + - + +
1039F LEU 5.8 0.7 - - - +
1042F ALA* 4.9 10.4 - - + +
1043F VAL* 4.6 25.6 - - + +
1046F LEU* 4.8 13.5 - - + -
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Residues in contact with LEU 929 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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867F LEU* 5.2 10.3 - - + +
871F ARG* 4.9 12.6 - - + -
925F SER 2.9 18.4 + - - +
926F GLY* 3.7 6.5 - - - +
928F THR* 1.3 76.7 - - - +
930F LYS* 1.3 57.3 + - - +
932F LEU* 3.3 6.3 + - - +
933F LEU* 2.9 31.1 + - - +
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Residues in contact with LYS 930 (chain F).
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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926F GLY 2.9 17.4 + - - +
927F GLU* 3.7 6.7 - - - +
929F LEU* 1.3 77.9 - - - +
931F THR* 1.3 57.6 + - - +
933F LEU* 3.3 5.7 + - - +
934F ALA* 2.9 30.4 + - - +
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Residues in contact with THR 931 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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927F GLU 2.9 18.0 + - - -
928F THR* 3.7 7.4 - - - -
930F LYS* 1.3 75.8 - - - +
932F LEU* 1.3 61.7 + - - +
934F ALA* 3.6 16.3 + - - +
935F LEU* 3.8 6.4 + - - +
988F LEU* 3.7 34.1 - - - +
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Residues in contact with LEU 932 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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928F THR* 2.9 20.1 + - + +
929F LEU* 3.7 7.0 - - - +
931F THR* 1.3 78.6 - - - +
933F LEU* 1.3 62.0 + - - +
935F LEU* 3.4 18.4 + - - +
936F GLY 4.3 1.6 + - - -
937F CYS* 5.3 1.4 + - - +
1043F VAL* 6.0 5.6 - - + -
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Residues in contact with LEU 933 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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929F LEU 2.9 17.7 + - - +
930F LYS* 3.9 6.3 - - - +
932F LEU* 1.3 72.9 - - - +
934F ALA* 1.3 64.3 + - - +
935F LEU 3.1 3.6 + - - -
936F GLY* 3.3 13.0 + - - -
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Residues in contact with ALA 934 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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930F LYS 2.9 17.5 + - - +
931F THR* 3.8 10.5 - - - +
932F LEU 3.3 0.4 - - - -
933F LEU* 1.3 76.5 - - - +
935F LEU* 1.3 62.5 + - - +
936F GLY 3.3 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
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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