Contacts of the helix formed by residues 914 - 934 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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906B CYS* 5.4 6.8 - - + -
913B LEU* 1.3 80.3 - - - +
915B GLU* 1.3 65.9 + - - +
916B PRO* 3.2 10.5 - - + -
917B GLU* 3.6 3.7 + - + +
918B ARG* 3.3 21.0 + - - +
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Residues in contact with GLU 915 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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914B PRO* 1.3 76.3 - - - +
916B PRO* 1.3 57.2 - - - +
918B ARG* 3.5 6.3 + - - +
919B ASN* 2.9 31.4 + - - +
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Residues in contact with PRO 916 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
914B PRO* 3.2 7.3 - - + -
915B GLU* 1.3 78.2 - - - +
917B GLU* 1.3 59.3 + - - +
919B ASN* 3.3 6.0 + - + +
920B TYR* 2.9 28.6 + - - +
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Residues in contact with GLU 917 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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882B TRP* 5.0 9.0 - - + -
906B CYS* 4.2 24.6 - - + +
908B VAL 5.0 2.5 - - - +
910B PHE* 4.6 3.5 - - - +
913B LEU* 3.7 28.3 - - + -
914B PRO* 3.6 3.2 + - - +
915B GLU 3.5 0.2 - - - -
916B PRO* 1.3 78.9 - - - +
918B ARG* 1.3 58.8 + - - +
920B TYR* 3.3 10.2 + - - +
921B ASN* 2.9 30.4 + - - +
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Residues in contact with ARG 918 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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910B PHE* 4.0 31.6 - - + +
914B PRO 3.3 16.1 + - - +
915B GLU* 3.8 7.2 - - - +
916B PRO 3.3 0.4 - - - -
917B GLU* 1.3 79.0 - - - +
919B ASN* 1.3 56.3 + - - +
921B ASN* 3.3 2.4 + - - +
922B LEU* 2.9 40.1 + - + +
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Residues in contact with ASN 919 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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915B GLU 2.9 19.1 + - - +
916B PRO* 3.7 4.9 - - + +
918B ARG* 1.3 75.8 - - - +
920B TYR* 1.3 58.2 + - - +
922B LEU* 3.3 9.9 + - - +
923B GLN* 2.9 29.6 + - - +
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Residues in contact with TYR 920 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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878B ILE* 6.3 3.4 - - + -
882B TRP* 4.2 40.1 - + + -
916B PRO 2.9 16.9 + - - +
917B GLU* 3.7 8.1 - - - +
919B ASN* 1.3 77.3 - - - +
921B ASN* 1.3 63.1 + - + +
923B GLN* 3.3 6.5 + - + +
924B MET* 2.9 38.3 + - + +
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Residues in contact with ASN 921 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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875B ALA* 3.5 29.5 - - + +
878B ILE* 5.8 2.7 - - + -
879B HIS* 5.2 5.4 - - + +
910B PHE* 4.2 17.9 - - + -
917B GLU 2.9 17.0 + - - +
918B ARG 3.7 4.7 - - - +
920B TYR* 1.3 82.2 - - + +
922B LEU* 1.3 58.2 + - + +
924B MET* 3.3 6.1 + - - +
925B SER* 2.9 30.3 + - - -
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Residues in contact with LEU 922 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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871B ARG* 5.9 1.6 - - + +
872B GLU* 6.1 3.8 - - - -
875B ALA* 5.0 9.4 - - + -
910B PHE* 5.7 9.6 - - + -
918B ARG* 2.9 26.8 + - + +
919B ASN* 3.7 8.5 - - - +
920B TYR 3.3 0.2 - - - -
921B ASN* 1.3 75.5 - - + +
923B GLN* 1.3 57.2 + - - +
925B SER* 3.3 6.4 + - - -
926B GLY* 2.9 25.8 + - - -
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Residues in contact with GLN 923 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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919B ASN 2.9 17.4 + - - +
920B TYR* 3.7 7.9 - - + +
922B LEU* 1.3 77.4 - - - +
924B MET* 1.3 57.5 + - - +
926B GLY* 3.3 1.3 + - - -
927B GLU* 2.9 29.5 + - - +
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Residues in contact with MET 924 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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878B ILE* 4.9 15.3 - - + -
920B TYR* 2.9 32.2 + - + +
921B ASN* 3.7 7.4 - - - +
923B GLN* 1.3 76.5 - - - +
925B SER* 1.3 58.0 + - - +
927B GLU* 3.3 6.5 + - - +
928B THR* 2.9 34.7 + - - +
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Residues in contact with SER 925 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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871B ARG* 3.2 39.9 - - - +
874B LEU* 4.3 7.4 - - - +
875B ALA* 3.7 12.5 - - - +
921B ASN 2.9 17.6 + - - -
922B LEU* 3.7 7.9 - - - -
923B GLN 3.3 0.2 - - - -
924B MET* 1.3 77.1 - - - +
926B GLY* 1.3 57.0 + - - +
928B THR* 3.3 6.3 + - - -
929B LEU* 2.9 29.8 + - - +
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Residues in contact with GLY 926 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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871B ARG* 5.1 2.4 - - - +
922B LEU 2.9 15.5 + - - -
923B GLN* 3.8 3.6 - - - -
925B SER* 1.3 78.6 - - - +
927B GLU* 1.3 56.5 + - - +
929B LEU* 3.3 6.7 + - - +
930B LYS* 2.9 29.8 + - - +
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Residues in contact with GLU 927 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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923B GLN 2.9 17.2 + - - +
924B MET* 3.7 7.4 - - - +
926B GLY* 1.3 75.7 - - - +
928B THR* 1.3 57.6 + - - +
930B LYS* 3.3 5.8 + - - +
931B THR* 2.9 30.1 + - - -
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Residues in contact with THR 928 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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874B LEU* 4.9 7.1 - - + +
924B MET* 2.9 19.8 + - - +
925B SER* 3.7 7.1 - - - -
927B GLU* 1.3 77.6 - - - +
929B LEU* 1.3 56.5 + - - +
931B THR* 3.3 6.3 + - - -
932B LEU* 2.9 29.0 + - + +
1039B LEU 5.8 0.7 - - - +
1042B ALA* 4.9 10.8 - - + +
1043B VAL* 4.6 26.0 - - + +
1046B LEU* 4.8 13.5 - - + -
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Residues in contact with LEU 929 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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867B LEU* 5.2 10.1 - - + +
871B ARG* 4.9 13.2 - - + -
925B SER 2.9 17.1 + - - +
926B GLY* 3.7 6.7 - - - +
927B GLU 3.3 0.2 - - - -
928B THR* 1.3 76.1 - - - +
930B LYS* 1.3 56.9 + - - +
932B LEU* 3.3 7.0 + - - +
933B LEU* 2.9 30.3 + - - +
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Residues in contact with LYS 930 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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926B GLY 2.9 17.6 + - - +
927B GLU* 3.7 6.7 - - - +
929B LEU* 1.3 77.5 - - - +
931B THR* 1.3 57.0 + - - +
933B LEU* 3.3 5.3 + - - +
934B ALA* 2.9 30.7 + - - +
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Residues in contact with THR 931 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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927B GLU 2.9 18.1 + - - -
928B THR* 3.7 7.0 - - - -
930B LYS* 1.3 75.4 - - - +
932B LEU* 1.3 62.6 + - - +
934B ALA* 3.6 16.1 + - - +
935B LEU* 3.8 6.4 + - - +
988B LEU* 3.7 32.9 - - - +
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Residues in contact with LEU 932 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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928B THR* 2.9 20.1 + - + +
929B LEU* 3.7 6.3 - - - +
930B LYS 3.2 0.2 - - - -
931B THR* 1.3 77.5 - - - +
933B LEU* 1.3 60.3 + - - +
935B LEU* 3.4 19.0 + - - +
936B GLY 4.3 1.4 + - - -
937B CYS* 5.3 1.7 + - - +
1043B VAL* 6.0 5.8 - - + -
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Residues in contact with LEU 933 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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929B LEU 2.9 17.4 + - - +
930B LYS* 3.3 5.8 + - - +
932B LEU* 1.3 72.5 - - - +
934B ALA* 1.3 64.7 + - - +
935B LEU 3.1 3.6 + - - -
936B GLY* 3.3 13.2 + - - +
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Residues in contact with ALA 934 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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930B LYS 2.9 18.3 + - - +
931B THR* 3.8 10.1 - - - +
932B LEU 3.3 0.6 - - - -
933B LEU* 1.3 77.5 - - - +
935B LEU* 1.3 61.5 + - - +
936B GLY* 3.3 0.7 - - - -
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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