Contacts of the helix formed by residues 1022 - 1039 (chain N) in PDB entry 2JA7
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 THR1022 (chain N).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
761M MET* 5.3 0.2 - - - -
762N ASN* 3.1 19.6 + - - +
766N ARG* 4.3 12.8 - - - -
984N HIS* 3.3 27.0 - - - +
986N GLN* 3.3 30.3 - - - +
1017N ILE* 4.3 17.0 + - + +
1020N ARG* 3.6 21.1 - - + -
1021N MET* 1.3 73.4 - - - +
1023N VAL* 1.3 61.4 + - - +
1024N ALA 3.5 0.2 - - - -
1025N HIS* 3.7 9.1 - - + +
1026N LEU* 4.2 3.6 + - - +
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Residues in contact with VAL1023 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
666M ILE* 4.0 10.1 - - + -
669M THR* 4.7 10.5 - - + +
761M MET* 3.9 31.0 - - + -
804M TYR* 4.1 28.0 - - + +
805M LEU* 4.8 7.9 - - + +
761N HIS 3.4 11.7 + - - +
1017N ILE* 6.4 0.2 - - + -
1021N MET 4.7 1.1 - - - -
1022N THR* 1.3 71.9 - - - +
1024N ALA* 1.3 58.6 + - - +
1025N HIS 3.1 2.2 - - - -
1026N LEU* 2.5 50.5 + - + +
1027N ILE* 2.8 25.3 + - + -
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Residues in contact with ALA1024 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
757N PRO 3.3 26.5 - - - +
758N PHE* 3.5 24.7 - - + +
761N HIS* 3.7 9.4 + - + +
762N ASN* 3.1 18.0 + - - +
984N HIS* 3.4 6.5 - - + -
1023N VAL* 1.3 77.4 - - - +
1025N HIS* 1.3 64.6 + - - +
1027N ILE* 2.9 6.0 + - - +
1028N GLU* 2.7 26.0 + - - +
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Residues in contact with HIS1025 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
825N VAL* 5.3 2.5 - - + -
827N ILE* 4.3 15.8 - - + +
982N SER* 3.0 31.6 - - - -
984N HIS* 3.1 30.9 + + + -
986N GLN* 4.2 13.8 - - + +
1012N ILE* 3.8 22.4 - - + +
1017N ILE* 4.8 6.7 - - + +
1022N THR* 3.7 17.0 + - + +
1024N ALA* 1.3 80.2 - - - +
1026N LEU* 1.3 66.9 + - - +
1028N GLU* 3.3 11.5 + - - +
1029N CYS* 3.4 11.3 + - + +
1086N PHE* 6.2 0.2 - + - -
1090N THR* 4.3 18.3 + - + +
1092N TYR* 3.5 20.8 + - - -
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Residues in contact with LEU1026 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
664M THR* 4.2 4.3 - - + +
665M GLY* 3.8 24.0 - - - -
666M ILE* 3.5 33.0 - - + +
669M THR* 4.6 10.1 - - + -
827N ILE* 4.0 15.9 - - + -
1017N ILE* 4.4 28.7 - - + -
1022N THR 4.5 6.5 - - - +
1023N VAL* 2.5 32.2 + - + +
1025N HIS* 1.3 77.3 + - - +
1027N ILE* 1.3 60.6 + - - +
1029N CYS* 3.3 5.0 - - - +
1030N LEU 3.7 0.9 + - - -
1086N PHE* 3.2 40.2 - - + -
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Residues in contact with ILE1027 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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666M ILE* 3.9 19.5 - - + -
805M LEU 4.3 1.3 - - - +
758N PHE* 2.9 32.1 - - + -
761N HIS* 3.9 39.3 - - + +
1023N VAL* 2.8 24.2 + - + +
1024N ALA* 2.9 3.1 + - - +
1026N LEU* 1.3 67.6 - - - +
1028N GLU* 1.3 69.5 + - - +
1029N CYS 2.7 3.8 + - - -
1030N LEU* 2.8 19.9 + - + +
1031N LEU* 2.9 14.9 + - + +
1051N THR 6.2 1.3 - - - -
1052N VAL* 3.8 28.0 - - + -
1055N ILE* 4.9 7.6 - - + -
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Residues in contact with GLU1028 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
757N PRO* 3.0 25.2 - - + +
758N PHE* 4.1 5.9 - - - -
804N GLY* 4.8 6.0 + - - -
983N ARG* 2.8 30.6 + - - +
984N HIS* 3.5 8.8 + - - -
1024N ALA 2.7 15.3 + - - +
1025N HIS* 3.4 10.5 - - - +
1027N ILE* 1.3 70.7 - - - +
1029N CYS* 1.3 57.8 + - - +
1031N LEU* 3.5 8.3 + - - +
1032N SER* 2.8 46.5 + - - +
1090N THR* 3.1 15.2 - - + +
1091N TYR* 2.5 35.0 + - - +
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Residues in contact with CYS1029 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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825N VAL* 5.3 2.9 - - - -
827N ILE* 5.9 0.2 - - - -
1025N HIS* 3.4 6.5 + - + +
1026N LEU 3.3 4.6 + - - +
1027N ILE 2.7 4.4 + - - -
1028N GLU* 1.3 72.2 - - - +
1030N LEU* 1.3 68.5 + - - +
1032N SER* 2.8 3.8 + - - -
1033N LYS* 2.6 25.0 + - - +
1086N PHE* 3.1 39.0 - - + -
1087N PHE 4.1 2.7 - - - -
1088N GLY* 3.3 43.5 - - - -
1089N PRO 3.3 12.0 - - - +
1090N THR* 3.9 8.7 + - - +
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Residues in contact with LEU1030 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
666M ILE* 3.9 22.0 - - + -
1026N LEU 3.7 3.7 + - - +
1027N ILE* 2.8 16.8 + - + +
1029N CYS* 1.3 79.2 - - - +
1031N LEU* 1.3 62.3 + - - +
1033N LYS* 2.9 15.7 + - + +
1034N VAL* 3.0 14.6 + - - +
1052N VAL* 3.9 21.8 - - + -
1055N ILE* 4.0 21.1 - - + -
1056N SER* 4.1 14.1 - - - +
1059N LEU* 3.8 13.7 - - + -
1066N SER 4.3 2.0 - - - +
1067N ARG* 3.5 6.1 - - - +
1068N GLY* 3.4 36.3 - - - +
1086N PHE* 4.2 6.7 - - + -
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Residues in contact with LEU1031 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
758N PHE* 3.3 33.4 - - + -
804N GLY* 4.8 7.9 - - - -
1027N ILE 2.9 9.7 + - - +
1028N GLU* 3.7 8.7 - - - +
1030N LEU* 1.3 77.4 - - - +
1032N SER* 1.3 57.6 + - - +
1034N VAL* 3.1 10.7 - - + +
1035N ALA* 2.9 25.7 + - + +
1042N GLY* 3.7 27.1 - - - -
1043N ASP 3.5 13.0 - - - +
1044N ALA* 3.5 17.5 - - + -
1050N ILE* 5.8 0.7 - - + -
1055N ILE* 3.5 28.1 - - + +
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Residues in contact with SER1032 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
803N LEU* 3.0 41.5 - - - +
804N GLY* 3.4 12.3 + - - -
822N ASN* 4.9 1.0 + - - -
1028N GLU* 2.8 31.7 + - - +
1029N CYS 2.8 2.0 + - - -
1031N LEU* 1.3 67.9 - - - +
1033N LYS* 1.3 54.5 + - - +
1034N VAL 2.8 5.2 - - - -
1035N ALA* 4.3 2.2 - - - +
1036N ALA* 2.7 37.2 + - - +
1089N PRO* 3.6 14.8 - - - -
1090N THR* 4.9 0.7 - - - -
1091N TYR 5.5 0.3 + - - -
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Residues in contact with LYS1033 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1029N CYS* 2.6 18.5 + - - +
1030N LEU* 3.4 10.8 - - + +
1032N SER* 1.3 72.6 - - - +
1034N VAL* 1.3 58.6 + - - +
1036N ALA* 4.2 3.8 - - - +
1037N LEU* 3.3 24.8 - - + +
1059N LEU* 3.8 17.7 - - + +
1064N TYR* 4.2 21.7 - - - +
1068N GLY* 2.6 34.3 + - - +
1069N PHE 4.0 0.8 + - - -
1070N GLU* 2.4 34.7 + - - +
1087N PHE 3.4 16.7 + - - +
1088N GLY* 4.3 1.1 - - - -
1089N PRO* 3.5 15.8 - - + +
44V TYR* 3.4 25.5 - - + -
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Residues in contact with VAL1034 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1030N LEU 3.0 11.2 + - - +
1031N LEU* 3.1 16.8 - - + +
1032N SER 2.8 0.6 - - - -
1033N LYS* 1.3 76.0 - - - +
1035N ALA* 1.3 57.9 - - + +
1036N ALA 2.6 2.6 + - - -
1037N LEU* 2.4 36.2 + - - +
1038N SER* 3.1 17.0 + - - +
1055N ILE* 3.9 16.8 - - + +
1058N LEU* 4.7 17.7 - - + -
1059N LEU* 3.6 40.4 - - + +
1062N HIS* 5.1 5.8 + - + -
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Residues in contact with ALA1035 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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803N LEU* 4.5 10.1 - - + +
1031N LEU 2.9 13.9 + - - +
1032N SER* 4.1 6.3 - - - +
1034N VAL* 1.3 78.2 - - + +
1036N ALA* 1.3 57.2 + - - +
1037N LEU 3.2 0.2 - - - -
1038N SER* 3.5 13.0 - - - -
1039N GLY* 2.9 22.7 + - - -
1040N ASN 3.2 23.7 + - - +
1041N GLU* 4.6 0.9 - - - -
1042N GLY* 3.5 17.3 - - - +
51V LEU* 3.3 12.3 - - - +
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Residues in contact with ALA1036 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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803N LEU* 4.2 20.4 - - + -
1032N SER 2.7 23.3 + - - +
1033N LYS* 4.2 7.2 - - - -
1034N VAL 2.6 4.9 + - - -
1035N ALA* 1.3 73.8 - - - +
1037N LEU* 1.3 56.3 + - - +
1089N PRO* 4.3 3.8 - - + -
44V TYR* 3.9 21.5 - - + -
47V ARG* 3.4 29.8 + - - +
48V ARG* 4.7 8.8 + - + -
51V LEU* 4.2 8.4 - - - +
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Residues in contact with LEU1037 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1033N LYS* 3.3 22.9 - - + +
1034N VAL 2.4 19.4 + - - +
1036N ALA* 1.3 72.4 - - - +
1038N SER* 1.3 59.4 + - - +
1039N GLY 3.3 1.6 - - - -
1059N LEU* 4.4 4.7 - - + -
1062N HIS* 3.8 40.8 - - + +
1064N TYR* 3.8 40.2 - - + +
33V GLY* 4.3 1.4 - - - -
42V LYS 4.7 4.9 - - - +
44V TYR* 4.3 16.2 - - + +
47V ARG* 3.0 43.6 + - - +
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Residues in contact with SER1038 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1034N VAL* 3.1 9.6 + - - +
1035N ALA* 3.5 13.2 + - - -
1037N LEU* 1.3 78.1 - - - +
1039N GLY* 1.3 64.2 + - - +
1040N ASN* 3.1 39.1 + - - +
1062N HIS* 4.2 17.9 - - - -
31V ASP* 5.3 1.6 - - - +
33V GLY* 3.6 16.1 + - - -
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Residues in contact with GLY1039 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1035N ALA 2.9 13.5 + - - -
1036N ALA 4.3 0.4 + - - -
1037N LEU 3.3 3.0 + - - -
1038N SER* 1.3 79.5 - - - +
1040N ASN* 1.3 59.6 + - - +
1041N GLU 3.9 2.4 + - - -
32V GLU* 3.1 33.1 - - - +
33V GLY* 3.9 11.7 - - - -
36V LEU* 5.4 0.9 - - - -
47V ARG* 4.5 2.0 - - - +
51V LEU* 3.4 23.3 - - - +
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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
------------------------------------------------------------
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