Contacts of the helix formed by residues 962 - 976 (chain D) in PDB entry 4AY6
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 962 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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936D MET* 3.8 14.6 - - - +
960D ALA* 3.4 2.5 - - - +
961D LYS* 1.3 88.5 + - - +
963D ARG* 1.3 67.6 + - - +
964D GLN* 3.3 13.2 - - - +
965D GLU* 2.9 38.7 + - - +
966D TYR* 2.9 21.1 + - - +
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Residues in contact with ARG 963 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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846D SER* 3.5 32.7 + - - -
850D MET* 3.8 36.4 - - + +
936D MET* 3.6 27.3 - - - +
962D ASN* 1.3 72.6 - - - +
964D GLN* 1.3 63.3 + - - +
966D TYR* 3.3 3.2 + - - +
967D GLU* 3.1 31.9 + - - +
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Residues in contact with GLN 964 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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857D ARG* 4.4 4.8 - - - +
962D ASN* 3.0 12.5 + - + +
963D ARG* 1.3 81.6 - - - +
965D GLU* 1.3 65.4 + - - +
967D GLU* 3.2 24.7 + - - +
968D ASP* 3.1 35.4 + - - +
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Residues in contact with GLU 965 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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959D ILE 4.4 4.1 - - - +
960D ALA* 3.9 8.1 - - + -
961D LYS* 3.0 46.3 + - - +
962D ASN* 2.9 23.4 + - - +
964D GLN* 1.3 72.9 - - - +
966D TYR* 1.3 64.4 - - - +
968D ASP* 2.9 11.3 + - + +
969D ILE* 2.9 42.8 + - + +
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Residues in contact with TYR 966 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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850D MET* 3.8 20.6 - - + -
851D TRP* 3.1 24.4 + + - -
854D ILE* 3.7 24.0 - - + -
912D LEU* 3.3 9.4 - - + +
913D ASP 3.0 34.9 + - - -
915D PRO* 4.8 5.4 - - + -
934D VAL* 3.6 36.5 - - + +
935D THR 4.0 7.0 - - - -
936D MET* 3.7 22.4 - - + -
960D ALA* 3.3 13.1 - - + +
962D ASN 2.9 11.9 + - - +
963D ARG* 3.3 13.2 - - - +
965D GLU* 1.3 77.4 - - - +
967D GLU* 1.3 65.5 + - - +
969D ILE* 3.3 3.1 + - - +
970D ALA* 3.1 21.1 + - - +
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Residues in contact with GLU 967 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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850D MET* 3.4 27.3 - - + +
853D ASN* 2.9 35.2 + - + +
854D ILE* 3.7 29.8 - - + -
857D ARG* 4.0 15.8 + - - +
963D ARG* 3.1 20.3 + - - +
964D GLN* 3.6 21.6 + - - +
966D TYR* 1.3 80.6 - - + +
968D ASP* 1.3 57.4 + - - +
970D ALA* 3.3 2.3 + - - +
971D VAL* 2.9 32.6 + - - +
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Residues in contact with ASP 968 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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857D ARG* 3.0 32.5 + - - +
964D GLN* 3.1 32.7 + - - +
965D GLU* 2.9 11.7 + - + +
967D GLU* 1.3 77.0 - - - +
969D ILE* 1.3 55.4 + - + +
971D VAL* 3.1 4.1 + - - +
972D LYS* 2.8 36.7 + - - +
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Residues in contact with ILE 969 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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934D VAL* 4.3 10.1 - - + -
957D GLU 3.4 28.3 - - - +
958D LEU* 4.3 13.2 - - + +
959D ILE 4.1 4.7 - - - +
960D ALA* 3.8 39.3 - - + +
965D GLU* 2.9 30.1 + - + +
966D TYR* 3.8 3.8 - - - +
968D ASP* 1.3 74.5 - - + +
970D ALA* 1.3 62.1 + - - +
972D LYS* 3.5 8.1 + - - +
973D LEU* 3.2 37.6 + - + +
979D TYR* 5.4 5.6 - - + +
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Residues in contact with ALA 970 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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834D TYR* 2.8 22.9 + - + -
854D ILE* 3.7 29.6 - - + -
912D LEU* 4.0 17.9 - - + -
934D VAL* 4.5 10.9 - - + +
966D TYR 3.1 13.2 + - - +
967D GLU 3.4 8.7 - - - +
969D ILE* 1.3 77.7 - - - +
971D VAL* 1.3 61.6 + - - +
973D LEU* 3.3 6.6 + - - +
974D GLY 3.1 9.2 + - - -
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Residues in contact with VAL 971 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
854D ILE* 4.2 13.7 - - + -
857D ARG* 3.9 55.0 - - + +
858D VAL* 3.7 23.6 - - + -
967D GLU 2.9 21.8 + - - +
968D ASP 3.7 3.4 - - - +
970D ALA* 1.3 73.9 - - - +
972D LYS* 1.3 67.2 + - - +
974D GLY* 3.0 2.8 + - - -
975D THR* 2.9 37.2 + - + +
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Residues in contact with LYS 972 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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968D ASP 2.8 17.2 + - - +
969D ILE* 3.7 8.3 - - - +
971D VAL* 1.3 76.6 - - - +
973D LEU* 1.3 56.9 + - - +
975D THR* 3.9 5.8 - - - -
976D ASP* 2.9 50.3 + - + +
979D TYR* 3.7 49.1 + - + -
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Residues in contact with LEU 973 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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910D VAL* 3.8 29.2 - - + -
932D PRO* 5.4 2.0 - - + -
934D VAL* 3.9 14.6 - - + -
958D LEU* 3.8 25.6 - - + -
969D ILE* 3.2 18.2 + - + +
970D ALA* 3.5 6.5 - - - +
971D VAL 3.2 0.2 - - - -
972D LYS* 1.3 78.8 - - - +
974D GLY* 1.3 59.3 + - - +
975D THR 3.6 0.2 + - - -
976D ASP 4.1 2.8 + - - +
977D LEU* 4.9 0.3 + - - +
979D TYR* 3.8 29.2 - - + -
980D LEU* 3.4 48.1 - - + +
983D VAL* 3.9 21.3 - - + -
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Residues in contact with GLY 974 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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832D ILE* 3.4 37.5 - - - +
834D TYR* 3.3 19.5 - - - -
858D VAL* 3.7 10.1 - - - +
910D VAL* 6.0 0.4 - - - -
970D ALA 3.1 5.9 + - - -
971D VAL 3.0 6.2 + - - -
973D LEU* 1.3 76.2 - - - +
975D THR* 1.3 61.6 + - - +
977D LEU* 4.3 5.0 - - - +
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Residues in contact with THR 975 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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857D ARG 4.5 6.1 - - - +
858D VAL* 3.8 18.8 - - + -
859D PRO* 5.4 4.3 - - + -
971D VAL* 2.9 28.9 + - + +
972D LYS* 3.4 7.8 + - - -
974D GLY* 1.3 82.5 - - - +
976D ASP* 1.3 69.2 + - - +
977D LEU* 3.1 18.7 + - - +
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Residues in contact with ASP 976 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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972D LYS* 2.9 31.5 + - + +
973D LEU 4.4 1.8 - - - -
975D THR* 1.3 78.4 + - - +
977D LEU* 1.3 50.3 + - - +
978D GLU* 3.5 11.8 + - - +
979D TYR* 2.8 33.4 + - + +
980D LEU* 2.8 32.9 + - - +
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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