Contacts of the helix formed by residues 984 - 1005 (chain A) in PDB entry 3O37
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 984 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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980A ASN* 3.6 9.5 - - - +
981A GLU* 2.7 34.4 + - - -
982A PRO 3.1 1.8 + - - -
983A ASP* 1.3 83.6 - - - +
985A GLU* 1.3 65.3 + - - +
986A VAL* 3.7 3.2 + - - +
987A ALA* 3.1 17.7 + - - +
988A ASN* 3.0 19.1 + - - -
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Residues in contact with GLU 985 (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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983A ASP 3.8 0.8 + - - +
984A SER* 1.3 72.9 - - - +
986A VAL* 1.3 61.0 + - + +
988A ASN* 3.4 9.9 + - - +
989A ALA* 2.9 27.7 + - - +
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Residues in contact with VAL 986 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
923A ALA* 4.7 15.0 - - + -
924A PHE* 3.6 14.9 - - + -
976A CYS* 3.4 9.2 - - - -
980A ASN* 3.2 37.9 - - - +
984A SER* 3.2 3.6 + - - +
985A GLU* 1.3 78.8 - - + +
987A ALA* 1.3 59.1 + - - +
989A ALA* 3.2 6.9 + - - +
990A GLY 2.8 25.1 + - - -
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Residues in contact with ALA 987 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
976A CYS* 3.9 13.3 - - - +
977A ALA* 5.6 4.5 - - - +
980A ASN* 4.1 11.6 - - + +
981A GLU 3.3 27.6 - - - +
982A PRO* 4.4 2.5 - - + -
983A ASP 4.2 6.7 - - - +
984A SER* 3.1 12.7 + - - +
986A VAL* 1.3 75.5 - - - +
988A ASN* 1.3 59.8 + - - +
990A GLY* 3.1 2.1 + - - -
991A ILE* 2.9 35.5 + - + +
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Residues in contact with ASN 988 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
920A MET* 5.7 0.2 - - - -
983A ASP* 3.2 49.6 + - - +
984A SER 3.0 13.9 + - - +
985A GLU* 3.7 9.7 + - - +
987A ALA* 1.3 75.5 - - - +
989A ALA* 1.3 64.8 + - - +
991A ILE* 3.3 10.3 + - - +
992A LYS* 3.0 28.8 + - + +
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Residues in contact with ALA 989 (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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920A MET* 3.8 42.1 - - - +
923A ALA* 5.5 3.4 - - + -
924A PHE* 3.9 9.4 - - + -
985A GLU 2.9 15.4 + - - +
986A VAL* 3.2 10.7 + - - +
988A ASN* 1.3 75.0 - - - +
990A GLY* 1.3 57.4 + - - +
992A LYS* 3.2 2.5 + - - +
993A LEU* 2.9 32.4 + - - +
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Residues in contact with GLY 990 (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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924A PHE* 3.6 17.2 - - - -
973A PHE* 3.8 10.0 - - - -
976A CYS* 3.7 12.1 - - - -
986A VAL 2.8 14.6 + - - -
987A ALA 3.1 4.5 + - - -
989A ALA* 1.3 77.2 - - - +
991A ILE* 1.3 56.6 + - - +
993A LEU* 3.8 1.7 - - - -
994A GLU* 2.8 32.2 + - - +
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Residues in contact with ILE 991 (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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977A ALA* 5.5 11.9 - - + -
987A ALA* 2.9 24.1 + - + +
988A ASN* 3.8 11.0 - - - +
989A ALA 3.3 0.2 - - - -
990A GLY* 1.3 76.1 - - - +
992A LYS* 1.3 59.0 + - + +
994A GLU* 3.4 18.5 + - - +
995A ASN* 3.0 51.3 + - - +
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Residues in contact with LYS 992 (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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918A HIS* 3.7 27.4 + - - -
919A GLU* 3.8 18.2 + - - -
920A MET* 4.0 20.6 - - + +
988A ASN* 3.0 20.4 + - + +
989A ALA 3.6 3.8 - - - +
991A ILE* 1.3 79.0 - - + +
993A LEU* 1.3 60.8 + - - +
995A ASN* 3.5 8.5 + - - +
996A TYR* 3.1 23.4 + - - +
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Residues in contact with LEU 993 (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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915A LEU* 4.0 20.1 - - + +
918A HIS* 3.7 39.5 - - + -
920A MET* 4.4 3.3 - - + +
921A SER* 3.8 22.2 - - - +
924A PHE* 3.7 31.6 - - + -
945A LEU* 4.9 8.1 - - + -
972A ILE* 5.8 0.2 - - + -
973A PHE* 3.8 17.9 - - + -
989A ALA 2.9 17.0 + - - +
990A GLY* 3.9 4.3 - - - +
992A LYS* 1.3 74.0 - - - +
994A GLU* 1.3 55.5 + - - +
996A TYR* 3.2 4.9 + - + +
997A PHE* 2.7 34.8 + - - +
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Residues in contact with GLU 994 (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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970A ARG* 5.7 3.3 - - - +
973A PHE* 3.6 45.4 - - + +
974A GLN* 5.8 2.1 + - - -
990A GLY 2.8 18.5 + - - +
991A ILE* 3.7 23.2 - - - +
993A LEU* 1.3 77.6 - - - +
995A ASN* 1.3 62.6 + - - +
997A PHE* 3.1 2.3 + - - +
998A GLU* 2.8 43.6 + - + +
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Residues in contact with ASN 995 (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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991A ILE* 3.0 42.4 + - - +
992A LYS* 3.8 8.0 - - - +
994A GLU* 1.3 81.1 - - - +
996A TYR* 1.3 63.8 + - - +
998A GLU* 3.4 6.3 + - - +
999A GLU* 3.1 29.4 + - + +
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Residues in contact with TYR 996 (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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914A PHE* 3.4 43.6 + - - -
915A LEU* 3.8 15.9 - - + -
918A HIS* 3.4 40.1 - + + -
992A LYS 3.1 12.5 + - - +
993A LEU* 3.4 7.9 - - + +
995A ASN* 1.3 81.0 - - - +
997A PHE* 1.3 61.9 + - - +
999A GLU* 3.2 9.9 + - + +
1000A LEU* 2.9 52.5 + - + +
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Residues in contact with PHE 997 (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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911A LEU* 4.2 24.0 - - + -
915A LEU* 3.9 28.3 - - + -
966A VAL* 4.4 5.6 - - + -
969A PHE* 3.5 42.2 - + + -
970A ARG* 4.3 10.3 - - + -
973A PHE* 3.6 25.4 - + + -
993A LEU 2.7 17.8 + - - +
994A GLU 3.3 6.7 - - - +
996A TYR* 1.3 74.3 - - - +
998A GLU* 1.3 82.9 + - - +
1000A LEU* 3.1 6.8 + - - +
1001A LEU* 2.9 54.5 + - + +
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Residues in contact with GLU 998 (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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970A ARG* 3.1 43.5 + - - +
973A PHE* 5.4 0.2 - - - -
994A GLU* 2.8 35.7 + - + +
995A ASN* 3.8 6.5 - - - +
997A PHE* 1.3 92.2 - - - +
999A GLU* 1.3 65.5 + - - +
1001A LEU* 3.3 8.0 + - - +
1002A LYS* 3.1 44.3 + - - +
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Residues in contact with GLU 999 (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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995A ASN* 3.1 16.6 + - + +
996A TYR* 3.2 12.5 + - + +
998A GLU* 1.3 75.5 - - - +
1000A LEU* 1.3 66.9 + - + +
1002A LYS* 3.1 38.8 + - - +
1003A ASN* 3.1 24.6 + - - +
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Residues in contact with LEU1000 (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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911A LEU* 3.6 21.1 - - + +
914A PHE* 3.5 47.3 - - + -
915A LEU* 3.7 19.5 - - + -
996A TYR* 2.9 52.0 + - + +
997A PHE* 3.3 6.7 - - - +
999A GLU* 1.3 76.3 - - + +
1001A LEU* 1.3 57.3 + - - +
1003A ASN* 3.1 14.2 + - - +
1004A LEU* 2.9 32.5 + - + +
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Residues in contact with LEU1001 (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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911A LEU* 3.8 25.3 - - + +
966A VAL* 3.8 28.0 - - + -
970A ARG* 3.5 27.8 - - - +
997A PHE* 2.9 33.2 + - + +
998A GLU* 3.5 13.2 - - - +
1000A LEU* 1.3 79.3 - - - +
1002A LYS* 1.3 56.6 + - + +
1004A LEU* 4.4 0.9 - - - +
1005A TYR* 2.8 54.2 + - + +
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Residues in contact with LYS1002 (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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998A GLU* 3.1 29.2 + - - +
999A GLU* 3.1 34.5 + - - +
1001A LEU* 1.3 77.2 - - + +
1003A ASN* 1.3 63.6 + - - +
1005A TYR 4.4 4.7 - - - -
1006A PRO* 3.5 23.2 - - - +
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Residues in contact with ASN1003 (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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999A GLU* 3.1 17.7 + - - +
1000A LEU* 3.1 18.1 + - + +
1002A LYS* 1.3 83.2 - - - +
1004A LEU* 1.3 64.8 + - + +
1006A PRO* 3.6 14.2 - - - +
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Residues in contact with LEU1004 (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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873A LEU* 4.0 27.6 - - + -
907A LYS* 2.8 52.3 + - + +
910A ARG* 4.0 21.3 - - + +
911A LEU* 3.4 42.0 - - + +
914A PHE* 5.4 4.3 - - + -
1000A LEU* 2.9 14.8 + - + +
1001A LEU* 4.3 1.1 - - - +
1003A ASN* 1.3 79.5 - - + +
1005A TYR* 1.3 73.6 + - + +
1006A PRO* 3.4 6.7 - - - +
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Residues in contact with TYR1005 (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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904A ASP* 2.7 31.9 + - - +
907A LYS* 3.4 38.3 - - + +
911A LEU* 4.7 2.0 - - + -
962A PRO* 3.6 19.4 - - + +
965A PHE* 3.5 27.7 - + - -
966A VAL* 5.6 0.4 - - + -
1001A LEU* 2.8 40.2 + - + +
1002A LYS* 3.8 7.3 - - - +
1004A LEU* 1.3 86.7 - - + +
1006A PRO* 1.3 68.0 - - - +
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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