Contacts of the strand formed by residues 996 - 1008 (chain A) in PDB entry 3PT6
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 ARG 996 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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943A VAL 3.6 0.7 - - - +
944A TYR* 3.7 0.9 - - - -
945A LEU* 2.5 41.2 + - + +
946A PRO 3.2 20.3 + - - +
947A PRO* 3.1 30.2 + - + +
950A PHE* 3.1 54.8 + - + +
951A THR* 5.3 2.8 - - - +
952A PHE* 3.6 30.0 - - - -
993A GLU* 3.1 35.3 + - - +
994A PRO* 3.4 10.9 + - - +
995A TYR* 1.3 75.4 - - - +
997A ILE* 1.3 64.5 + - - +
1026A ARG* 5.1 0.7 - - - +
1029A ASN* 5.0 4.4 + - - +
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Residues in contact with ILE 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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942A SER* 4.6 0.4 - - - -
943A VAL 3.4 9.6 - - - +
944A TYR* 4.0 13.7 - - + -
945A LEU* 5.8 0.7 - - - -
950A PHE* 3.9 10.1 - - - -
995A TYR 3.9 0.2 + - - -
996A ARG* 1.3 82.0 - - - +
998A GLY* 1.3 64.9 + - - +
1024A PHE* 3.0 46.6 + - + +
1026A ARG* 3.3 32.6 - - + +
1045A LEU* 3.8 22.7 - - + -
1063A CYS* 3.9 15.9 - - - -
1065A VAL* 4.2 3.8 - - + -
1086A PHE* 3.7 33.2 - - + -
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Residues in contact with GLY 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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942A SER* 3.3 4.4 - - - -
943A VAL* 2.9 33.5 + - - +
945A LEU* 5.6 1.0 - - - +
950A PHE* 5.2 1.5 - - - -
997A ILE* 1.3 77.9 - - - +
999A ARG* 1.3 61.0 + - - -
1000A ILE 3.9 0.5 + - - -
1021A LEU* 4.6 16.1 - - - +
1022A TYR 3.2 14.6 - - - -
1023A LYS* 4.7 1.1 - - - -
1024A PHE* 3.8 7.6 - - - -
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Residues in contact with ARG 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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940A GLY* 2.7 36.1 + - - +
941A ASP 3.6 2.7 - - - +
942A SER* 3.3 19.5 - - - -
998A GLY* 1.3 72.1 - - - -
1000A ILE* 1.3 69.9 + - - +
1001A LYS 3.2 0.9 + - - -
1021A LEU* 3.2 3.6 - - - -
1022A TYR* 2.8 52.1 + - + +
1024A PHE* 4.0 15.0 - - + -
1047A TRP* 3.1 35.6 - - + -
1065A VAL 4.5 13.0 + - - -
1066A GLU* 5.6 2.0 + - - -
1088A PHE* 4.2 11.5 - - - -
1105A HIS 5.1 2.2 + - - -
1106A ALA* 3.0 24.8 + - - -
1107A ARG 4.9 3.4 + - - -
1108A SER* 5.2 5.1 + - - -
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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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937A TYR* 4.5 7.9 - - + -
938A ARG 2.8 43.3 - - - +
939A LEU* 3.7 5.3 - - + +
940A GLY* 3.1 20.9 + - - +
941A ASP* 3.0 24.0 + - + +
943A VAL* 4.3 16.4 - - + -
999A ARG* 1.3 72.6 - - - +
1001A LYS* 1.3 62.3 + - - +
1002A GLU 5.0 0.4 - - - +
1003A ILE* 4.1 17.7 - - + -
1019A LEU* 3.7 24.9 - - + -
1020A ARG 4.6 0.4 - - - +
1021A LEU* 3.4 23.6 - - + -
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Residues in contact with LYS1001 (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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939A LEU* 3.3 15.0 - - - +
999A ARG 3.2 2.2 + - - +
1000A ILE* 1.3 73.6 - - - +
1002A GLU* 1.3 83.0 + - + +
1020A ARG* 2.6 31.5 + - + +
1021A LEU* 4.5 0.4 - - - +
1022A TYR* 3.0 45.2 + - + -
1051A GLU* 3.1 32.3 + - + +
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Residues in contact with GLU1002 (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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926A TYR* 3.7 32.6 + - + -
939A LEU* 3.7 4.9 - - - -
1001A LYS* 1.3 108.9 + - + +
1003A ILE* 1.3 64.8 + - - +
1004A HIS* 4.6 6.9 + - - +
1019A LEU* 3.4 6.1 - - - +
1020A ARG* 2.8 55.7 + - + +
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Residues in contact with ILE1003 (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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926A TYR* 3.4 6.1 - - - +
927A CYS* 2.7 46.5 + - + +
928A SER 4.1 26.2 - - - +
929A SER 4.4 0.9 - - - +
930A ILE* 3.7 26.2 - - + +
937A TYR 4.7 1.6 - - - +
939A LEU* 3.8 12.4 - - + +
1000A ILE* 4.1 23.8 - - + -
1002A GLU* 1.3 75.9 - - - +
1004A HIS* 1.3 63.0 + - - +
1017A ILE* 3.5 28.9 - - + -
1018A LYS 3.5 2.7 - - - -
1019A LEU* 3.4 20.0 - - + -
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Residues in contact with HIS1004 (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 ARG* 2.9 46.1 + - + -
925A VAL 3.1 13.9 - - - +
926A TYR* 3.5 39.5 - + + -
927A CYS* 4.4 0.9 - - - +
1002A GLU* 4.6 11.8 + - - +
1003A ILE* 1.3 76.7 - - - +
1005A CYS* 1.3 59.8 + - - +
1017A ILE* 4.6 1.8 - - - -
1018A LYS* 3.1 41.6 + - + +
1020A ARG* 5.0 15.5 - - + -
1053A VAL* 4.7 13.1 - - + +
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Residues in contact with CYS1005 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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914A VAL* 6.4 0.7 - - + -
924A ARG* 3.0 16.2 - - - -
925A VAL 2.7 29.2 + - - +
927A CYS* 5.0 9.7 - - - -
1004A HIS* 1.3 73.3 - - - +
1006A GLY* 1.3 62.2 + - - +
1012A VAL* 3.8 22.7 - - + -
1013A ASN 3.7 16.4 - - - +
1014A GLU* 5.2 0.2 - - - -
1016A ASP 3.2 6.5 - - - +
1017A ILE* 4.0 16.6 - - + +
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Residues in contact with GLY1006 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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923A GLY 4.2 3.1 - - - -
924A ARG* 3.4 21.6 - - - +
925A VAL* 5.1 2.3 + - - +
1005A CYS* 1.3 77.6 - - - +
1007A LYS* 1.3 56.6 + - - +
1012A VAL* 3.7 5.5 - - - +
1013A ASN* 2.8 30.0 + - - -
1016A ASP* 3.0 25.4 + - - -
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Residues in contact with LYS1007 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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920A GLU* 5.4 7.2 - - - +
923A GLY* 4.3 14.0 + - - +
925A VAL* 5.7 5.6 - - + -
1006A GLY* 1.3 74.3 - - - +
1008A LYS* 1.3 64.9 + - - +
1010A GLY* 5.3 4.0 - - - -
1011A LYS 3.1 17.3 - - - +
1012A VAL* 4.8 0.9 - - - -
1013A ASN* 3.8 5.2 - - - +
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Residues in contact with LYS1008 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1007A LYS* 1.3 76.3 - - - +
1009A LYS* 1.3 71.4 + - + +
1010A GLY 3.2 1.1 - - - +
1011A LYS* 2.7 27.1 + - - +
1012A VAL 5.2 0.5 - - - +
1013A ASN* 4.0 22.2 - - + +
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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