Contacts of the helix formed by residues 994 - 1013 (chain A) in PDB entry 5W0N
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 THR 994 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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992A PRO 5.3 1.8 - - - +
993A LEU* 1.3 77.6 - - - +
995A PRO* 1.3 74.0 - - + +
996A LYS* 3.7 9.1 + - - +
997A PHE* 3.1 23.8 + - - +
998A LEU* 3.0 25.6 + - - +
1314A PRO* 6.1 0.4 - - - +
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Residues in contact with PRO 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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993A LEU 4.6 1.8 - - - +
994A THR* 1.3 88.2 - - + +
996A LYS* 1.3 56.3 + - - +
998A LEU* 3.2 14.8 + - + +
999A ASN* 2.9 30.3 + - - +
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Residues in contact with LYS 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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994A THR* 3.2 8.9 - - - +
995A PRO* 1.3 80.4 - - - +
997A PHE* 1.3 61.7 + - - +
999A ASN* 3.5 7.0 + - - +
1000A ILE* 3.3 31.2 + - + +
1319A PRO* 5.9 3.4 - - + -
1320A LYS* 5.1 14.1 - - - +
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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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993A LEU* 3.6 32.5 - - + -
994A THR* 3.1 22.8 + - - +
996A LYS* 1.3 75.7 - - - +
998A LEU* 1.3 66.2 + - - +
1000A ILE* 3.1 12.7 + - + +
1001A LEU* 3.0 40.6 + - + +
1310A VAL 4.9 1.6 - - - -
1311A PHE 3.6 25.4 - - - -
1314A PRO* 3.9 36.8 - - + -
1318A PHE* 4.2 19.1 - + - -
1328A TYR* 6.1 0.4 - + - -
1329A PHE* 4.2 23.1 - + - -
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Residues in contact with LEU 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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993A LEU* 3.4 36.6 - - + +
994A THR 3.0 20.3 + - - +
995A PRO* 3.2 16.4 + - + +
997A PHE* 1.3 77.7 - - - +
999A ASN* 1.3 60.6 + - - +
1001A LEU* 3.4 13.6 + - + +
1002A ASP* 3.1 31.3 + - - +
1233A SER* 5.6 2.9 - - - +
1235A GLY* 5.0 0.2 - - - -
1236A GLN* 5.4 20.6 + - + +
1239A LEU* 6.0 0.4 - - + -
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Residues in contact with ASN 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 PRO 2.9 16.3 + - - +
996A LYS* 3.8 7.6 - - - +
997A PHE 3.2 0.4 - - - -
998A LEU* 1.3 73.8 - - - +
1000A ILE* 1.3 66.9 + - + +
1002A ASP* 3.3 16.4 + - - +
1003A GLN* 2.6 55.8 + - - +
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Residues in contact with ILE1000 (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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996A LYS* 3.3 23.0 + - + +
997A PHE* 3.1 18.6 + - + +
999A ASN* 1.3 75.1 - - - +
1001A LEU* 1.3 66.7 + - - +
1003A GLN* 3.2 10.3 + - - +
1004A VAL* 3.0 23.1 + - + +
1318A PHE* 4.0 18.4 - - + -
1319A PRO* 3.9 31.4 - - + -
1325A LYS* 4.3 24.9 - - + +
1329A PHE* 3.9 28.3 - - + -
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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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993A LEU* 4.3 13.2 - - + -
997A PHE* 3.0 46.7 + - + +
998A LEU* 3.7 13.2 - - + +
999A ASN 3.3 0.2 - - - -
1000A ILE* 1.3 75.1 - - - +
1002A ASP* 1.3 62.8 + - - +
1004A VAL* 3.3 5.8 + - + +
1005A CYS* 3.2 27.4 + - - -
1235A GLY* 3.8 25.4 - - - +
1236A GLN* 6.0 0.2 - - - -
1238A TRP* 5.6 2.9 - - + -
1239A LEU* 4.6 8.5 - - + -
1311A PHE* 3.7 44.9 - - + +
1329A PHE* 4.1 11.9 - - + -
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Residues in contact with ASP1002 (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 LEU* 3.1 17.6 + - - +
999A ASN* 3.5 21.7 + - - +
1000A ILE 3.2 0.2 - - - -
1001A LEU* 1.3 76.8 - - - +
1003A GLN* 1.3 61.1 + - + +
1005A CYS* 3.3 2.6 + - - +
1006A ILE* 3.1 35.7 + - + +
1233A SER* 2.9 30.5 + - - -
1234A VAL* 4.4 4.9 - - + +
1235A GLY* 2.7 36.2 + - - +
1236A GLN 3.9 0.2 + - - -
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Residues in contact with GLN1003 (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 ASN* 2.6 42.7 + - - +
1000A ILE* 3.2 13.6 + - - +
1002A ASP* 1.3 77.2 - - + +
1004A VAL* 1.3 59.2 + - + +
1006A ILE* 3.2 7.8 + - + +
1007A GLN* 2.8 38.8 + - + +
1325A LYS* 3.7 26.8 - - + +
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Residues in contact with VAL1004 (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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1000A ILE* 3.0 17.5 + - + +
1001A LEU* 3.8 6.7 - - - +
1002A ASP 3.3 0.2 - - - -
1003A GLN* 1.3 77.9 - - + +
1005A CYS* 1.3 64.3 + - - +
1007A GLN* 3.3 7.2 + - - +
1008A CYS* 3.1 23.0 + - - -
1150A THR* 5.8 0.4 - - + -
1311A PHE* 4.4 14.1 - - + -
1325A LYS* 4.4 17.5 - - + +
1326A MET* 4.1 10.3 - - - +
1329A PHE* 3.8 29.8 - - + -
1330A PHE* 3.7 31.9 - - + -
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Residues in contact with CYS1005 (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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1001A LEU 3.2 15.7 + - - -
1002A ASP 3.7 5.6 - - - +
1004A VAL* 1.3 81.1 - - - +
1006A ILE* 1.3 62.5 + - - +
1008A CYS* 3.4 11.4 + - - +
1009A TYR 3.6 4.2 + - - -
1146A TYR* 3.8 9.8 - - - +
1147A LEU* 4.9 0.4 - - - -
1150A THR* 3.2 31.3 + - - +
1234A VAL* 3.4 31.6 - - + -
1235A GLY* 4.2 2.5 - - - -
1238A TRP* 3.6 39.9 - - - -
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Residues in contact with ILE1006 (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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1002A ASP* 3.1 25.1 + - + +
1003A GLN* 3.8 7.4 - - + +
1005A CYS* 1.3 75.4 - - - +
1007A GLN* 1.3 61.7 + - - +
1009A TYR* 3.1 4.9 + - - +
1010A LYS* 3.0 47.2 + - + +
1146A TYR* 4.1 43.3 - - + +
1234A VAL* 4.6 10.3 - - + -
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Residues in contact with GLN1007 (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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1003A GLN* 2.8 25.1 + - + +
1004A VAL* 3.3 6.0 + - - +
1006A ILE* 1.3 75.5 - - - +
1008A CYS* 1.3 57.4 + - - +
1010A LYS* 3.2 35.5 - - - +
1011A ASP* 2.7 70.8 + - - +
1326A MET* 4.2 18.4 - - + -
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Residues in contact with CYS1008 (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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1004A VAL 3.1 19.1 + - - -
1005A CYS 3.5 9.9 - - - +
1006A ILE 3.2 0.2 - - - -
1007A GLN* 1.3 76.8 - - - +
1009A TYR* 1.3 60.8 + - - +
1012A PHE* 3.2 32.7 + - - +
1149A TYR* 3.7 7.3 - - - +
1150A THR* 3.8 23.6 - - - +
1153A VAL* 3.9 22.6 - - + +
1326A MET* 4.0 8.3 - - - -
1330A PHE* 3.8 33.7 - - - -
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Residues in contact with TYR1009 (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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1005A CYS 3.6 2.5 + - - +
1006A ILE 3.1 8.5 + - - +
1008A CYS* 1.3 77.7 - - - +
1010A LYS* 1.3 72.4 + - + +
1013A SER* 2.7 52.4 + - - -
1051A GLY 5.4 0.2 - - - -
1145A LYS* 4.1 33.6 + - + +
1146A TYR* 3.6 38.1 - + + -
1149A TYR* 3.5 45.0 - + + +
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Residues in contact with LYS1010 (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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1006A ILE* 3.0 33.0 + - + +
1007A GLN* 3.2 35.8 - - - +
1009A TYR* 1.3 90.9 - - + +
1011A ASP* 1.3 63.9 + - - +
1012A PHE 3.5 0.2 + - - -
1013A SER* 4.1 9.5 + - - +
1055A LYS* 5.2 1.6 - - - -
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Residues in contact with ASP1011 (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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1007A GLN* 2.7 50.0 + - - +
1010A LYS* 1.3 77.1 - - - +
1012A PHE* 1.3 81.4 + - + +
1013A SER 3.8 0.2 - - - -
1055A LYS* 3.3 19.5 - - - +
1326A MET* 4.3 18.4 - - - +
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Residues in contact with PHE1012 (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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1008A CYS* 3.2 22.8 + - - +
1009A TYR 3.5 1.4 + - - -
1010A LYS 3.4 0.2 - - - -
1011A ASP* 1.3 93.5 - - + +
1013A SER* 1.3 63.2 - - - +
1054A PHE* 3.2 29.9 - + + -
1055A LYS* 2.9 33.8 + - + +
1149A TYR* 4.4 1.3 - - - -
1153A VAL* 3.6 26.9 - - + -
1326A MET* 3.7 31.9 - - + -
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Residues in contact with SER1013 (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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1009A TYR* 2.7 39.7 + - - -
1010A LYS* 4.1 8.5 + - - +
1011A ASP 3.8 0.2 - - - -
1012A PHE* 1.3 78.3 + - - +
1014A PRO* 1.3 74.1 + - - +
1053A GLY 3.7 4.3 - - - -
1055A LYS* 3.2 18.3 + - - -
1149A TYR* 3.5 23.6 - - - -
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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