Contacts of the helix formed by residues 959 - 971 (chain A) in PDB entry 6UPY
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 959 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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879A GLU* 2.9 48.9 + - + +
880A LYS 5.3 4.4 + - - -
881A GLN* 3.4 11.5 - - - +
956A LEU 4.9 0.2 + - - -
957A PRO 4.3 0.2 - - - -
958A VAL* 1.3 71.8 - - - +
960A ILE* 1.3 59.1 + - - +
961A ARG* 3.1 18.4 + - - +
962A ARG* 2.7 58.5 + - - +
963A ILE* 3.4 16.5 + - - +
1052A GLN* 4.9 5.0 + - - +
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Residues in contact with ILE 960 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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881A GLN* 3.3 4.3 + - - +
958A VAL* 3.1 22.2 + - + +
959A ASN* 1.3 70.8 - - - +
961A ARG* 1.3 65.2 + - - +
963A ILE* 4.2 7.0 - - + -
964A ILE* 3.2 41.8 + - + +
1018A PHE* 4.1 21.3 - - + -
1021A LEU* 4.4 12.1 - - + -
1022A LEU* 4.2 20.6 - - + -
1025A ARG* 4.1 27.4 - - + +
1026A LEU* 4.9 5.4 - - + -
1035A TYR* 5.5 0.4 - - - +
1049A ILE* 4.0 27.4 - - + -
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Residues in contact with ARG 961 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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589A GLN* 5.3 7.4 - - - +
880A LYS 3.7 7.5 + - - -
881A GLN* 3.4 36.4 + - - +
882A SER* 3.7 11.0 + - - +
953A ASN* 5.9 1.4 - - - +
959A ASN* 3.1 15.5 + - - +
960A ILE* 1.3 78.7 - - - +
962A ARG* 1.3 59.1 + - + +
964A ILE* 4.0 5.9 + - - +
965A GLN* 2.8 37.2 + - - +
1025A ARG* 3.1 48.8 - - - +
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Residues in contact with ARG 962 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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587A HIS* 4.9 8.5 - - + +
631A HIS 4.9 0.2 + - - -
632A VAL* 3.9 35.1 + - - +
635A ARG* 3.4 24.3 - - - +
636A GLU* 2.3 39.9 + - - +
879A GLU* 2.3 36.6 + - - -
959A ASN* 2.7 39.8 + - - +
961A ARG* 1.3 73.9 - - + +
963A ILE* 1.3 65.2 + - - +
964A ILE 3.2 2.2 - - - -
965A GLN* 3.1 15.6 + - - +
966A ASN* 2.8 29.3 + - - +
1052A GLN* 4.4 9.7 - - - +
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Residues in contact with ILE 963 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
636A GLU* 5.0 6.5 - - - +
958A VAL* 4.1 10.8 - - + -
959A ASN 3.4 10.2 + - - +
960A ILE* 3.2 10.8 + - - +
962A ARG* 1.3 77.7 - - + +
964A ILE* 1.3 63.0 + - + +
966A ASN* 3.2 10.8 + - - +
967A ALA* 3.0 21.3 + - - +
1044A TRP* 4.0 2.0 - - + -
1045A VAL* 3.6 37.5 - - + -
1048A ASN* 3.7 29.6 - - + +
1049A ILE* 3.8 21.3 - - + +
1052A GLN* 3.3 26.9 - - - +
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Residues in contact with ILE 964 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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960A ILE* 3.2 38.7 + - + +
961A ARG* 4.2 6.1 - - - +
962A ARG 3.2 0.8 - - - -
963A ILE* 1.3 79.5 - - - +
965A GLN* 1.3 57.9 + - + +
967A ALA* 3.3 5.6 + - - +
968A GLN* 2.6 45.2 + - + +
1026A LEU* 4.8 2.7 - - + -
1035A TYR* 3.7 55.6 - - + +
1037A LEU* 5.4 7.9 - - + +
1045A VAL* 4.2 20.4 - - + -
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Residues in contact with GLN 965 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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587A HIS* 3.4 52.0 + - + +
589A GLN* 4.3 26.7 + - - +
961A ARG* 2.8 33.2 + - - +
962A ARG* 3.1 19.8 + - - +
964A ILE* 1.3 78.9 - - + +
966A ASN* 1.3 66.8 + - - +
968A GLN* 3.7 8.8 - - + +
969A GLN* 3.0 26.5 + - - +
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Residues in contact with ASN 966 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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585A GLY 4.6 11.1 - - - +
587A HIS* 5.3 4.9 - - - +
636A GLU* 3.2 40.5 + - - +
962A ARG* 2.8 17.1 + - - +
963A ILE* 3.2 12.6 + - - +
965A GLN* 1.3 78.3 - - - +
967A ALA* 1.3 50.5 + - - +
969A GLN* 3.2 2.3 + - - +
970A THR* 2.6 44.2 + - - +
1044A TRP* 3.5 20.8 - - + -
1048A ASN* 4.9 2.2 - - - +
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Residues in contact with ALA 967 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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963A ILE 3.0 9.7 + - - +
964A ILE* 3.9 3.4 - - - +
966A ASN* 1.3 77.2 - - - +
968A GLN* 1.3 62.6 + - - +
969A GLN 3.3 0.5 + - - -
970A THR* 4.3 0.2 - - - -
971A PHE* 3.4 37.4 + - + +
973A ILE* 4.1 4.1 - - - +
1037A LEU* 4.8 6.5 - - + -
1041A ALA* 4.5 7.3 - - + +
1044A TRP* 3.4 28.4 - - + -
1045A VAL* 3.7 20.6 - - + -
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Residues in contact with GLN 968 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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587A HIS* 6.1 0.7 - - - -
964A ILE* 2.6 29.5 + - + +
965A GLN* 3.7 11.9 - - + +
966A ASN 3.3 0.4 - - - -
967A ALA* 1.3 73.1 - - - +
969A GLN* 1.3 60.1 + - - +
971A PHE 3.5 9.4 - - - +
972A HIS* 4.4 0.3 - - - -
973A ILE* 3.7 31.5 + - + +
975A HIS* 3.9 24.1 + - - -
1035A TYR* 4.7 10.8 - - - +
1037A LEU* 5.5 3.3 - - + +
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Residues in contact with GLN 969 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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585A GLY* 5.0 5.2 - - - -
587A HIS* 5.3 8.5 - - + +
608A ILE* 5.3 9.8 - - + +
609A ASP* 3.7 40.6 + - + +
965A GLN 3.0 16.8 + - - +
966A ASN* 4.1 1.7 - - - +
968A GLN* 1.3 80.8 - - - +
970A THR* 1.3 69.0 + - - +
971A PHE 3.5 1.1 - - - -
972A HIS* 3.9 33.3 + - + +
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Residues in contact with THR 970 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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966A ASN* 2.6 33.3 + - - +
967A ALA* 4.3 4.7 - - - -
969A GLN* 1.3 78.1 + - - +
971A PHE* 1.3 86.4 + - + +
972A HIS* 3.6 9.4 + - - -
1044A TRP* 4.4 13.0 - - + -
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Residues in contact with PHE 971 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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967A ALA* 3.4 16.4 + - + +
968A GLN 3.5 2.1 - - - +
969A GLN 4.1 1.1 - - - -
970A THR* 1.3 93.5 - - + +
972A HIS* 1.3 67.7 + - - +
973A ILE* 2.9 21.3 + - + +
1038A THR* 5.6 2.0 - - - +
1040A GLN* 4.3 27.4 - - + +
1041A ALA* 3.4 43.3 - - + -
1044A TRP* 4.0 40.2 - + + -
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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