Contacts of the helix formed by residues 97 - 113 (chain 3) in PDB entry 6Q8O
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 SER 97 (chain 3).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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513 ARG* 4.0 15.4 + - - -
943 ASP* 2.2 34.2 + - - -
953 THR 3.7 0.8 - - - -
963 LEU* 1.3 80.3 - - - +
983 ASP* 1.3 66.3 + - - +
993 VAL* 4.2 11.2 - - - -
1003 VAL* 2.9 22.1 + - - +
1013 ARG* 3.0 11.4 + - - +
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Residues in contact with ASP 98 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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963 LEU 3.5 1.1 + - - +
973 SER* 1.3 73.5 - - - +
993 VAL* 1.3 59.0 + - + +
1013 ARG* 2.2 44.1 + - - +
1023 GLU* 2.9 32.7 + - - +
1403 TYR* 3.8 20.4 + - + +
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Residues in contact with VAL 99 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3971 ARG* 4.8 8.9 + - - +
513 ARG* 6.3 5.8 - - - +
793 LEU* 4.8 22.2 - - + -
973 SER* 3.1 8.4 - - - -
983 ASP* 1.3 80.4 - - + +
1003 VAL* 1.3 62.6 + - + +
1023 GLU* 3.3 11.5 + - + +
1033 ALA* 2.9 23.2 + - - +
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Residues in contact with VAL 100 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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493 LEU 3.9 11.6 - - - +
503 VAL* 4.2 2.7 - - - -
513 ARG* 3.7 23.6 - - + +
793 LEU* 4.4 8.7 - - + -
943 ASP 3.3 22.7 - - - +
953 THR* 3.5 27.1 - - - +
973 SER* 2.9 18.9 + - - +
993 VAL* 1.3 78.4 - - + +
1013 ARG* 1.3 62.7 + - - +
1033 ALA* 3.2 6.5 + - - +
1043 GLN* 3.0 41.3 + - - +
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Residues in contact with ARG 101 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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953 THR 4.6 7.6 - - - +
963 LEU* 3.5 27.1 + - - +
973 SER 3.0 12.0 + - - +
983 ASP* 2.2 34.3 + - - +
1003 VAL* 1.3 75.0 - - - +
1023 GLU* 1.3 57.6 + - - +
1043 GLN* 3.4 14.5 + - - +
1053 ALA* 3.0 30.0 + - - +
1373 TYR* 4.4 5.5 - - + +
1403 TYR* 3.2 40.9 - - + +
1413 GLU* 4.5 8.7 - - - +
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Residues in contact with GLU 102 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3921 PRO* 5.6 5.7 - - - +
3931 LEU* 3.9 12.5 - - + +
3971 ARG* 5.8 2.9 - - - +
983 ASP* 2.9 19.0 + - - +
993 VAL* 3.6 11.3 - - + +
1013 ARG* 1.3 77.2 - - - +
1033 ALA* 1.3 58.4 + - - +
1053 ALA* 3.4 2.9 + - - +
1063 GLY* 2.9 27.0 + - - -
1403 TYR* 4.6 25.1 - - + +
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Residues in contact with ALA 103 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3931 LEU* 4.3 6.2 - - - +
3971 ARG* 3.4 31.6 - - - +
493 LEU* 5.0 14.1 - - + -
793 LEU* 4.0 15.3 - - + -
993 VAL 2.9 15.4 + - - +
1003 VAL* 3.7 4.9 - - - +
1023 GLU* 1.3 75.8 - - - +
1043 GLN* 1.3 64.0 + - - +
1063 GLY* 3.4 0.5 + - - -
1073 MET* 3.0 31.4 + - + +
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Residues in contact with GLN 104 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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293 ASP 4.8 1.9 + - - +
303 VAL* 3.9 8.3 - - - +
313 PRO* 3.2 31.8 - - + +
473 MET* 4.0 10.6 - - - +
493 LEU* 3.6 20.7 - - + +
503 VAL* 5.1 0.7 - - - +
953 THR* 4.9 5.2 + - - +
1003 VAL* 3.0 31.2 + - - +
1013 ARG* 3.8 15.3 - - - +
1033 ALA* 1.3 76.9 - - + +
1053 ALA* 1.3 62.0 + - - +
1073 MET* 3.4 5.0 + - - +
1083 VAL* 3.0 29.9 + - - +
1373 TYR* 3.1 35.6 - - + +
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Residues in contact with ALA 105 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1013 ARG 3.0 17.8 + - - +
1023 GLU* 3.9 3.8 - - - +
1043 GLN* 1.3 76.2 - - - +
1063 GLY* 1.3 62.6 + - - +
1083 VAL* 3.2 4.5 + - - +
1093 GLU* 3.0 22.7 + - - +
1373 TYR 3.5 20.8 + - - +
1383 GLY* 4.0 6.7 - - - -
1393 LEU* 3.7 18.3 + - - +
1403 TYR* 4.1 12.8 - - + +
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Residues in contact with GLY 106 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3931 LEU* 3.6 26.9 - - - -
1023 GLU 2.9 11.5 + - - -
1053 ALA* 1.3 77.4 - - - +
1073 MET* 1.3 56.8 + - - +
1093 GLU* 3.2 13.2 + - - +
1103 PHE* 3.0 37.8 + - - -
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Residues in contact with MET 107 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3571 THR* 5.3 0.4 - - - -
3581 PRO* 3.4 38.4 - - + -
3931 LEU* 3.7 19.5 - - + +
3971 ARG* 4.3 7.6 - - + +
453 CYS 3.7 14.1 - - - +
463 ARG* 3.4 28.3 - - + +
473 MET* 3.5 11.4 - - + -
493 LEU* 4.1 17.3 - - + -
1033 ALA* 3.0 23.3 + - + +
1043 GLN* 3.8 5.2 - - - +
1063 GLY* 1.3 75.7 - - - +
1083 VAL* 1.3 57.9 + - - +
1103 PHE* 3.3 13.5 + - + +
1113 THR* 2.9 32.8 + - - +
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Residues in contact with VAL 108 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
313 PRO* 5.3 0.9 - - + -
333 PHE* 5.8 0.7 - - + -
473 MET* 3.5 23.1 - - + -
1043 GLN 3.0 21.4 + - - +
1053 ALA* 3.5 11.2 - - - +
1073 MET* 1.3 76.2 - - - +
1093 GLU* 1.3 63.1 + - - +
1113 THR* 3.1 2.6 + - - -
1123 LEU* 2.9 29.3 + - + +
1303 LEU* 5.4 1.8 - - + -
1333 ARG* 4.3 18.4 - - + +
1343 THR* 3.5 38.1 - - + +
1373 TYR* 4.7 10.8 - - + -
1383 GLY* 4.7 6.7 - - - +
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Residues in contact with GLU 109 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3661 PHE* 4.5 12.5 - - - -
3901 LEU* 6.1 0.7 - - - +
3931 LEU* 5.7 3.3 - - - +
1053 ALA 3.0 13.1 + - - +
1063 GLY* 3.2 13.4 + - - +
1083 VAL* 1.3 77.9 - - - +
1103 PHE* 1.3 69.8 + - + +
1123 LEU* 3.3 7.8 + - - +
1133 LEU* 2.9 31.3 + - + +
1543 TYR 5.0 5.8 - - - +
1553 THR* 5.0 1.2 + - - -
1563 ARG* 3.7 47.1 + - - +
1573 PHE 4.6 1.7 + - - -
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Residues in contact with PHE 110 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3571 THR* 4.6 5.2 - - + -
3581 PRO* 4.2 10.8 - - + -
3611 GLU* 3.1 25.1 - - + +
3621 GLY* 4.5 13.5 - - - -
3661 PHE* 4.0 19.3 - + - -
3901 LEU* 3.7 23.8 - - + -
3931 LEU* 3.5 49.8 - - + -
3941 ILE* 4.3 14.1 - - + -
1063 GLY 3.0 22.3 + - - -
1073 MET* 3.4 24.2 - - - +
1083 VAL 3.2 0.2 - - - -
1093 GLU* 1.3 82.8 - - + +
1113 THR* 1.3 60.6 + - - +
1133 LEU* 3.0 24.0 - - + +
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Residues in contact with THR 111 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3571 THR* 3.2 24.9 + - + +
3611 GLU* 4.8 3.9 - - - +
333 PHE* 4.2 11.3 - - + -
453 CYS* 5.0 0.3 + - - +
473 MET* 3.0 16.9 - - - +
1073 MET 2.9 17.9 + - - -
1083 VAL* 3.6 4.5 - - - -
1103 PHE* 1.3 76.3 - - - +
1123 LEU* 1.3 61.9 + - - +
1133 LEU 3.3 0.9 + - - -
1143 ASN* 4.1 5.5 + - - +
1153 HIS* 4.8 3.3 + - - +
1303 LEU* 4.3 9.1 - - + +
1823 ILE* 3.7 48.8 - - + +
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Residues in contact with LEU 112 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1083 VAL* 2.9 24.1 + - + +
1093 GLU* 3.6 6.1 - - - +
1113 THR* 1.3 71.7 - - - +
1133 LEU* 1.3 65.7 + - - +
1143 ASN 3.0 4.9 + - - -
1153 HIS* 3.3 26.0 + - + +
1303 LEU* 3.5 39.7 - - + -
1343 THR* 3.3 35.4 - - + +
1613 ARG* 3.5 6.6 + - - -
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Residues in contact with LEU 113 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3611 GLU* 3.7 44.0 - - + +
3651 GLY* 4.6 2.2 - - - -
3661 PHE* 4.1 24.2 - - + +
1093 GLU* 2.9 22.2 + - + +
1103 PHE* 3.0 18.8 - - + +
1113 THR 3.1 1.0 - - - -
1123 LEU* 1.3 75.8 - - - +
1143 ASN* 1.3 65.3 + - - +
1573 PHE* 3.9 46.7 - - + -
1613 ARG* 2.2 32.5 + - - +
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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