Contacts of the helix formed by residues 961 - 973 (chain A) in PDB entry 6A5T
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 961 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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636A ARG* 5.9 0.4 - - - +
880A GLU* 2.3 38.8 + - - +
882A GLN* 2.9 27.4 + - - +
959A PRO 3.5 0.4 + - - -
960A VAL* 1.3 74.5 - - - +
962A LEU* 1.3 76.2 + - - +
963A ARG* 3.0 36.5 + - - +
964A ARG* 3.1 35.4 + - + +
965A ILE* 3.4 22.5 + - - +
1027A ARG* 5.2 0.7 + - - -
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Residues in contact with LEU 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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882A GLN* 4.1 4.7 + - - +
960A VAL 3.3 11.2 + - - +
961A ASN* 1.3 74.7 + - - +
963A ARG* 1.3 59.5 + - - +
965A ILE* 2.6 31.3 + - + +
966A ILE* 2.8 19.9 + - + +
1020A PHE* 5.3 1.6 - - + -
1023A LEU* 4.2 12.8 - - + -
1024A VAL* 3.9 38.4 - - + +
1027A ARG* 4.1 32.5 - - + +
1028A LEU* 5.8 4.3 - - + -
1051A ILE* 3.4 43.1 - - + -
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Residues in contact with ARG 963 (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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590A GLN* 6.1 0.4 - - - -
880A GLU* 4.6 0.6 + - - -
881A ARG 5.4 3.6 + - - -
882A GLN* 5.0 9.5 - - - +
883A THR* 4.8 8.9 + - - +
961A ASN* 3.0 33.4 + - - +
962A LEU* 1.3 77.5 - - - +
964A ARG* 1.3 58.2 + - - +
966A ILE* 3.3 12.0 + - + +
967A GLN* 2.9 47.5 + - + +
1027A ARG* 3.8 28.9 - - - +
1037A PHE* 6.3 2.9 - - + -
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Residues in contact with ARG 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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588A HIS* 5.6 7.4 + - + +
628A GLY* 6.3 0.8 - - - -
632A HIS* 5.8 1.4 - - - -
633A THR* 3.6 28.4 + - - +
636A ARG* 4.3 14.0 - - - +
637A GLU* 2.9 37.5 + - - +
880A GLU* 2.4 45.7 + - - -
961A ASN* 3.1 28.5 + - - +
962A LEU 2.7 4.6 + - - -
963A ARG* 1.3 75.8 - - - +
965A ILE* 1.3 66.5 + - + +
967A GLN* 3.2 22.0 + - + +
968A ASN* 2.9 28.0 + - - +
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Residues in contact with ILE 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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637A GLU* 5.5 4.7 - - - +
960A VAL* 3.6 29.6 - - + -
961A ASN 3.4 8.7 + - - +
962A LEU* 2.6 14.6 + - - +
964A ARG* 1.3 75.3 - - + +
966A ILE* 1.3 56.8 + - + +
968A ASN* 3.3 8.7 + - - +
969A ALA* 2.9 25.8 + - - +
1046A TRP* 4.5 6.5 - - + -
1047A VAL* 4.0 27.4 - - + -
1050A THR* 3.5 35.9 - - + -
1051A ILE* 4.0 14.8 - - + -
1054A GLN* 4.0 7.6 - - - +
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Residues in contact with ILE 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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962A LEU* 2.8 24.0 + - + +
963A ARG* 3.7 11.4 - - - +
965A ILE* 1.3 78.9 - - + +
967A GLN* 1.3 59.7 + - + +
969A ALA* 3.0 9.3 + - - +
970A GLN* 2.8 35.6 + - + +
1027A ARG* 5.1 2.7 - - + -
1028A LEU* 3.5 32.5 - - + -
1037A PHE* 3.6 43.7 - - + -
1039A LEU* 5.0 9.8 - - + +
1047A VAL* 4.6 17.7 - - + -
1051A ILE* 6.0 0.4 - - + -
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Residues in contact with GLN 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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588A HIS* 4.2 27.5 + - + +
589A LEU* 5.8 0.4 - - - +
590A GLN* 3.8 30.6 + - - +
963A ARG* 2.9 35.2 + - - +
964A ARG* 3.2 32.4 - - + +
966A ILE* 1.3 74.5 - - + +
968A ASN* 1.3 65.3 + - - +
970A GLN* 3.2 23.4 + - - +
971A GLN* 3.0 22.9 + - - +
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Residues in contact with ASN 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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586A GLY* 4.3 9.6 + - - +
587A ILE 6.2 0.2 - - - -
588A HIS* 3.5 22.4 + - - -
637A GLU* 3.2 35.3 + - - -
964A ARG* 2.9 20.2 + - - +
965A ILE* 3.6 10.7 - - - +
967A GLN* 1.3 77.5 - - - +
969A ALA* 1.3 62.2 + - - +
971A GLN* 3.1 6.8 + - - +
972A ILE* 2.9 31.0 + - + +
1046A TRP* 4.6 14.4 - - + -
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Residues in contact with ALA 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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965A ILE 2.9 9.9 + - - +
966A ILE* 3.0 13.7 + - - +
968A ASN* 1.3 79.2 - - - +
970A GLN* 1.3 63.0 + - - +
971A GLN 3.2 0.2 + - - -
972A ILE* 3.4 7.0 + - - -
973A PHE* 3.4 19.6 + - - +
975A LEU* 5.3 0.3 - - - +
1039A LEU* 4.7 10.8 - - + -
1043A ALA* 4.6 9.6 - - + +
1046A TRP* 4.1 15.1 - - + -
1047A VAL* 3.5 32.3 - - + -
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Residues in contact with GLN 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 ILE* 2.8 27.7 + - + +
967A GLN* 3.3 22.8 - - - +
969A ALA* 1.3 72.9 - - - +
971A GLN* 1.3 62.9 + - - +
974A HIS* 3.0 18.7 + - - -
975A LEU* 3.1 25.5 + - - +
976A ASP* 4.9 13.1 - - - +
1036A GLU 5.4 1.2 + - - -
1037A PHE* 4.4 37.5 - - - +
1039A LEU* 4.9 5.1 - - + +
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Residues in contact with GLN 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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586A GLY* 5.3 4.5 - - - -
587A ILE 4.5 0.2 - - - +
588A HIS* 2.3 42.2 + - + +
609A VAL* 5.5 1.3 - - - +
610A ASP* 2.1 44.1 + - - +
967A GLN 3.0 15.6 + - - +
968A ASN* 3.1 8.2 + - - +
970A GLN* 1.3 75.8 - - - +
972A ILE* 1.3 72.5 + - + +
974A HIS* 3.2 17.3 + - - +
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Residues in contact with ILE 972 (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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968A ASN* 2.9 20.1 + - + +
969A ALA* 3.4 1.1 + - - +
971A GLN* 1.3 77.5 - - + +
973A PHE* 1.3 89.9 + - + +
974A HIS* 2.8 27.5 + - - -
1046A TRP* 4.2 31.4 - - + -
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Residues in contact with PHE 973 (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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969A ALA* 3.4 11.9 + - - +
970A GLN 3.8 0.2 - - - -
971A GLN 3.4 0.4 - - - -
972A ILE* 1.3 94.1 - - + +
974A HIS* 1.3 73.9 + - - +
975A LEU* 3.0 25.1 + - + +
977A ARG* 5.3 0.7 + - - -
1040A ASN* 5.2 4.7 - - - +
1042A ASP* 4.6 19.5 - - + -
1043A ALA* 3.6 34.8 - - + -
1046A TRP* 4.4 25.8 - + + -
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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