Contacts of the helix formed by residues 1001 - 1017 (chain A) in PDB entry 6DBU
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 SER1001 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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999A ARG* 3.9 6.1 - - - +
1000A GLN* 1.3 75.7 - - - +
1002A LYS* 1.3 52.1 + - - +
1003A THR* 2.5 24.6 + - - -
1004A PHE* 2.6 39.3 + - - -
1005A GLU* 3.1 8.0 + - - +
14F C 3.3 41.3 + - - -
15F T 4.5 9.6 - - - -
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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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572A ILE* 3.6 41.4 - - + +
636A PRO* 4.9 24.8 - - + +
681A PHE* 4.7 13.6 - - + -
994A ARG* 6.1 0.7 - - - +
1001A SER* 1.3 68.5 - - - +
1003A THR* 1.3 62.5 + - + +
1004A PHE 3.4 0.4 - - - -
1005A GLU* 3.6 28.3 + - - +
1006A LEU* 4.3 7.3 + - - +
15F T 5.3 18.0 + - - -
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Residues in contact with THR1003 (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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572A ILE* 4.7 7.6 - - + +
574A ARG* 3.1 40.9 + - - +
1001A SER* 2.5 12.7 + - - +
1002A LYS* 1.3 75.8 - - + +
1004A PHE* 1.3 99.6 + - + -
1006A LEU 4.6 0.2 + - - -
1007A GLU* 4.5 3.8 + - - +
14F C 6.2 3.1 - - - -
15F T 5.8 3.4 - - - +
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Residues in contact with PHE1004 (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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574A ARG* 5.9 1.3 - - - -
999A ARG* 3.0 59.5 - - + +
1001A SER* 2.6 25.3 + - - +
1003A THR* 1.3 95.0 + - - +
1005A GLU* 1.3 63.2 + - - +
1006A LEU 3.3 2.5 - - - -
1007A GLU* 3.2 22.4 + - + +
1008A ASP* 3.0 26.2 + - - +
13F A 5.8 6.7 - - - -
14F C 5.3 9.6 - - - -
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Residues in contact with GLU1005 (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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681A PHE* 4.5 7.2 - - + -
994A ARG* 2.7 49.7 + - + +
998A ALA* 3.9 20.3 - - + +
999A ARG* 4.3 10.7 - - - +
1000A GLN* 4.7 8.1 - - - +
1001A SER 3.1 19.1 + - - +
1002A LYS* 3.6 30.2 + - - +
1003A THR 3.5 0.6 - - - -
1004A PHE* 1.3 78.0 - - - +
1006A LEU* 1.3 59.0 + - + +
1008A ASP* 3.3 2.5 + - - +
1009A ILE* 3.0 32.6 + - + +
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Residues in contact with LEU1006 (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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572A ILE* 3.9 24.5 - - + +
573A SER* 4.3 9.6 - - - -
574A ARG* 3.9 18.3 - - + +
679A LEU* 3.6 43.7 - - + +
680A MET 5.1 0.7 - - - +
681A PHE* 3.5 42.2 - - + +
990A PHE* 4.5 12.6 - - + -
1002A LYS 4.3 6.4 + - - +
1003A THR 4.6 0.4 + - - +
1005A GLU* 1.3 77.3 - - + +
1007A GLU* 1.3 67.1 + - - +
1009A ILE* 3.3 4.5 + - + +
1010A LEU* 2.9 27.2 + - - +
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Residues in contact with GLU1007 (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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553A ILE* 3.5 37.6 - - + +
574A ARG* 4.1 16.9 + - - +
999A ARG* 4.8 7.1 + - - -
1003A THR 4.6 3.1 - - - +
1004A PHE* 3.2 33.1 + - - +
1006A LEU* 1.3 78.3 - - - +
1008A ASP* 1.3 64.6 + - - +
1010A LEU* 3.8 0.6 - - - +
1011A LYS* 3.0 34.0 + - + +
24E C 5.5 4.2 + - - +
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Residues in contact with ASP1008 (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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997A ASN* 4.1 16.6 - - - +
998A ALA* 4.8 0.7 - - - -
999A ARG* 3.1 48.7 + - - +
1004A PHE 3.0 12.6 + - - +
1005A GLU 3.8 3.8 - - - +
1007A GLU* 1.3 82.8 - - - +
1009A ILE* 1.3 67.5 + - - +
1011A LYS* 3.3 13.1 + - - +
1012A HIS* 3.0 31.4 + - + +
23E G 3.7 24.9 - - - +
24E C 4.2 6.8 + - - +
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Residues in contact with ILE1009 (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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679A LEU* 4.4 7.0 - - + -
990A PHE* 3.4 41.7 - - + -
993A PHE* 4.2 17.5 - - + +
994A ARG* 3.5 51.6 - - + +
997A ASN* 5.7 2.0 - - + -
998A ALA* 5.2 5.8 - - - +
1005A GLU* 3.0 25.4 + - + +
1006A LEU* 3.8 6.3 - - + +
1008A ASP* 1.3 75.2 - - - +
1010A LEU* 1.3 59.6 + - - +
1012A HIS* 3.4 3.6 + - - +
1013A HIS* 2.9 33.5 + - + +
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Residues in contact with LEU1010 (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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553A ILE* 3.9 15.5 - - + -
574A ARG* 4.5 5.4 - - + +
575A ARG* 4.1 22.9 - - - +
576A PHE* 3.5 47.8 - - + -
676A PRO* 4.1 30.3 - - + +
677A LEU 4.8 2.5 - - - +
679A LEU* 4.4 17.3 - - + -
1006A LEU 2.9 17.2 + - - +
1007A GLU 3.8 1.8 - - - +
1009A ILE* 1.3 80.7 - - - +
1011A LYS* 1.3 64.0 + - - +
1013A HIS* 3.3 4.2 + - - +
1014A TRP* 2.9 22.2 + - - +
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Residues in contact with LYS1011 (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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490A ARG* 4.6 6.1 - - - +
523A ARG* 5.9 3.8 - - - +
526A GLU* 4.2 12.4 + - - +
530A LEU* 3.6 42.2 - - + -
553A ILE* 4.4 10.8 - - + -
576A PHE* 5.0 0.7 - - - -
1007A GLU* 3.0 22.3 + - + +
1008A ASP* 3.3 15.2 + - - +
1010A LEU* 1.3 78.9 - - - +
1012A HIS* 1.3 80.5 + - - +
1014A TRP* 3.4 2.0 + - - +
1015A LEU* 3.0 36.3 + - + +
23E G 4.9 1.7 + - - -
24E C 3.6 27.1 + - - -
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Residues in contact with HIS1012 (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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490A ARG* 2.9 33.1 + - - -
491A VAL* 4.1 16.5 - - + +
495A LEU 5.7 0.2 - - - -
497A CYS* 4.9 0.4 - - - -
993A PHE* 3.8 22.6 - + + -
997A ASN* 2.8 44.9 + - + +
1008A ASP* 3.0 19.8 + - + +
1009A ILE* 4.0 2.9 - - - +
1011A LYS* 1.3 94.8 + - + +
1013A HIS* 1.3 65.8 + - - +
1015A LEU* 3.3 7.9 + - + +
1016A TYR* 2.9 23.7 + - - +
23E G 4.0 17.5 - - - -
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Residues in contact with HIS1013 (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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641A ARG* 4.5 24.0 + - - -
671A GLU 5.3 2.2 - - - -
674A CYS 4.3 8.8 + - - -
676A PRO* 3.3 37.0 - - + +
679A LEU* 5.8 1.8 - - + -
986A GLY* 4.6 7.1 + - - -
989A LEU* 3.8 31.7 - - + +
990A PHE* 5.6 9.4 - + + -
993A PHE* 3.9 16.2 - + + -
1009A ILE* 2.9 20.5 + - + +
1010A LEU* 3.7 5.8 - - - +
1012A HIS* 1.3 76.5 - - - +
1014A TRP* 1.3 58.2 + - - +
1016A TYR* 2.8 27.0 + + - -
1017A THR* 3.0 16.7 + - + +
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Residues in contact with TRP1014 (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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529A LEU* 3.4 19.8 + - + -
530A LEU* 3.9 13.7 - - + -
531A PRO* 3.6 19.1 - - + +
576A PHE* 4.1 20.4 - + + -
581A ALA* 3.5 30.1 - - + -
584A SER* 3.7 23.1 - - - -
585A ALA* 3.9 6.5 - - + -
644A PHE* 4.8 3.1 - + - -
675A ARG* 3.2 58.8 - - + +
676A PRO* 3.7 20.1 - - - +
1010A LEU* 2.9 18.2 + - + +
1011A LYS 3.8 3.4 - - - +
1013A HIS* 1.3 76.0 - - - +
1015A LEU* 1.3 68.7 + - + +
1017A THR* 3.2 22.6 + - - +
1018A SER* 3.8 8.9 + - - -
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Residues in contact with LEU1015 (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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487A LEU* 3.5 35.0 - - + -
491A VAL* 4.1 22.2 - - + +
526A GLU* 4.0 14.8 - - + +
529A LEU* 4.1 17.3 - - + -
530A LEU* 3.4 32.1 - - + +
1011A LYS* 3.0 22.3 + - + +
1012A HIS* 3.5 11.7 - - + +
1013A HIS 3.2 0.2 - - - -
1014A TRP* 1.3 82.5 - - + +
1016A TYR* 1.3 61.3 + - - +
1017A THR 3.2 0.7 + - - -
1018A SER* 3.7 7.0 + - - -
1021A LEU* 3.8 26.5 - - + +
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Residues in contact with TYR1016 (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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491A VAL* 3.7 15.0 - - + +
492A ASN* 3.2 41.5 - - - -
494A PHE* 5.2 8.8 - + - -
671A GLU* 5.1 8.7 + - + +
672A LEU* 3.6 28.6 - - + +
989A LEU* 3.4 46.4 - - + +
993A PHE* 4.3 14.8 - + + -
1012A HIS 2.9 12.5 + - - +
1013A HIS* 2.8 18.8 + + - +
1015A LEU* 1.3 75.5 - - - +
1017A THR* 1.3 59.7 + - - +
1018A SER 3.6 2.1 + - - +
1021A LEU* 6.3 0.2 - - - -
1022A GLN* 4.4 13.1 + - + +
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Residues in contact with THR1017 (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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671A GLU 4.8 2.7 - - - -
672A LEU* 3.2 26.0 + - - +
673A SER* 5.2 0.2 - - - -
674A CYS 3.5 11.9 + - - -
675A ARG* 2.5 48.3 + - + +
676A PRO* 3.8 20.4 - - + -
1013A HIS* 3.0 21.3 + - - +
1014A TRP* 3.5 14.6 - - + +
1015A LEU 3.2 0.8 - - - -
1016A TYR* 1.3 80.6 - - - +
1018A SER* 1.3 54.2 + - - +
1019A LYS 4.1 0.5 + - - -
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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