Contacts of the helix formed by residues 1022 - 1039 (chain B) in PDB entry 3HOU
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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
761A MET* 5.2 0.4 - - - -
762B ASN* 2.8 20.8 + - - -
766B ARG* 4.2 16.2 - - - -
984B HIS* 3.0 26.2 - - - +
986B GLN* 3.2 31.6 - - - +
1017B ILE* 4.4 13.9 + - + +
1020B ARG* 3.7 15.3 - - + -
1021B MET* 1.3 74.4 - - - +
1023B VAL* 1.3 63.3 + - - +
1024B ALA 3.2 1.6 - - - -
1025B HIS* 3.3 12.0 + - + +
1026B LEU* 4.0 4.6 + - - +
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Residues in contact with VAL1023 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
666A ILE* 3.8 17.0 - - + -
669A THR* 4.7 9.4 - - + +
761A MET* 3.9 30.3 - - + +
804A TYR* 4.1 27.6 - - + +
805A LEU* 4.6 7.6 - - - +
761B HIS 3.5 13.5 + - - +
1021B MET 3.6 0.6 - - - -
1022B THR* 1.3 73.9 - - - +
1024B ALA* 1.3 68.5 + - - +
1026B LEU* 2.7 25.1 + - + +
1027B ILE* 3.0 30.4 + - + +
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Residues in contact with ALA1024 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
757B PRO 3.4 5.8 - - - +
758B PHE* 3.4 28.5 - - + +
761B HIS* 3.5 7.4 + - + +
762B ASN* 3.1 33.3 + - - +
984B HIS* 3.4 10.7 - - + -
1022B THR 3.2 0.8 - - - -
1023B VAL* 1.3 76.0 - - - +
1025B HIS* 1.3 53.0 + - - +
1027B ILE* 3.0 4.5 + - - +
1028B GLU* 2.7 36.6 + - - +
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Residues in contact with HIS1025 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
825B VAL* 5.3 1.6 - - + -
827B ILE* 4.8 7.5 - - + +
982B SER* 3.1 37.6 - - - -
984B HIS* 3.0 30.2 + + + -
986B GLN* 4.3 15.9 - - + +
1012B ILE* 3.6 28.0 - - + +
1017B ILE* 4.8 8.6 - - + +
1022B THR* 3.3 18.7 + - + +
1023B VAL 3.0 0.2 - - - -
1024B ALA* 1.3 80.2 - - - +
1026B LEU* 1.3 67.3 + - - +
1027B ILE 3.1 0.2 + - - -
1028B GLU* 3.2 10.0 + - - +
1029B CYS* 3.3 12.3 + - + +
1086B PHE* 5.7 1.5 - + - -
1090B THR* 4.2 21.3 - - + +
1092B TYR* 3.5 11.3 + + - -
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Residues in contact with LEU1026 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
664A THR* 4.4 1.6 - - - +
665A GLY* 3.8 15.0 - - - +
666A ILE* 3.4 41.8 - - + +
669A THR* 4.7 11.7 - - + -
761A MET* 5.9 0.2 - - - -
827B ILE* 4.1 15.9 - - + -
1017B ILE* 4.2 30.5 - - + -
1022B THR 4.5 3.4 - - - +
1023B VAL* 2.7 30.4 + - + +
1025B HIS* 1.3 76.6 - - - +
1027B ILE* 1.3 59.2 + - - +
1029B CYS* 3.4 4.5 - - - +
1030B LEU 3.4 2.9 + - - -
1086B PHE* 3.2 42.2 - - + -
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Residues in contact with ILE1027 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
666A ILE* 3.9 9.9 - - + -
805A LEU 4.6 0.7 - - - +
758B PHE* 2.9 37.9 - - + -
761B HIS* 3.8 31.2 - - + +
1023B VAL* 3.0 31.4 + - + +
1024B ALA 3.6 1.8 - - - +
1026B LEU* 1.3 74.3 - - - +
1028B GLU* 1.3 55.3 + - - +
1029B CYS 2.6 17.0 + - - -
1030B LEU* 2.8 6.7 + - + +
1031B LEU* 2.7 22.3 + - - +
1051B THR 6.1 0.4 - - - -
1052B VAL* 3.7 25.6 - - + +
1055B ILE* 4.3 14.8 - - + -
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Residues in contact with GLU1028 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
757B PRO* 3.3 20.1 - - + +
758B PHE* 4.1 6.8 - - - -
804B GLY* 5.2 3.4 - - - -
983B ARG* 2.6 36.8 + - - +
984B HIS* 3.1 21.6 + - - +
1024B ALA 2.7 20.8 + - - +
1025B HIS 3.7 4.7 - - - +
1027B ILE* 1.3 69.9 - - - +
1029B CYS* 1.3 56.0 + - - +
1031B LEU* 4.0 7.4 - - - +
1032B SER* 2.9 36.0 + - - +
1044B ALA* 5.6 0.7 - - - -
1090B THR* 3.7 14.9 - - + +
1091B TYR* 2.8 28.2 + - - +
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Residues in contact with CYS1029 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
825B VAL* 5.0 2.0 - - - -
1025B HIS* 3.3 8.5 + - + +
1026B LEU 3.4 11.9 - - - +
1027B ILE 2.6 4.9 + - - -
1028B GLU* 1.3 72.8 - - - +
1030B LEU* 1.3 67.9 + - - +
1031B LEU 2.9 0.9 - - - -
1032B SER* 2.8 3.3 + - - -
1033B LYS* 2.7 25.4 + - - +
1086B PHE* 3.6 27.4 - - + -
1087B PHE 3.7 19.3 - - - -
1088B GLY* 3.5 26.5 - - - -
1089B PRO 3.4 11.6 - - - +
1090B THR* 3.9 9.4 - - + +
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Residues in contact with LEU1030 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
666A ILE* 4.1 13.7 - - + -
1026B LEU 3.4 7.9 + - - +
1027B ILE* 2.8 14.1 + - + +
1029B CYS* 1.3 77.0 - - - +
1031B LEU* 1.3 63.3 + - - +
1033B LYS* 3.6 7.7 + - + +
1034B VAL* 3.4 16.5 + - - +
1052B VAL* 4.5 12.8 - - + +
1055B ILE* 3.6 26.5 - - + +
1056B SER* 3.5 26.5 - - - +
1059B LEU* 3.7 13.6 - - + +
1066B SER 3.8 4.7 - - - +
1067B ARG* 3.3 32.8 - - - +
1068B GLY* 3.3 12.3 - - - +
1086B PHE* 4.1 6.3 - - + -
1087B PHE 5.9 0.2 - - - +
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Residues in contact with LEU1031 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
758B PHE* 3.3 22.4 - - + -
804B GLY* 4.7 5.4 - - - -
1027B ILE 2.7 20.2 + - - +
1028B GLU* 4.0 4.5 - - - +
1029B CYS 2.8 0.4 + - - -
1030B LEU* 1.3 72.0 - - - +
1032B SER* 1.3 58.9 + - - +
1034B VAL* 3.1 9.1 + - + +
1035B ALA* 3.0 25.3 + - + +
1042B GLY* 3.7 25.1 - - - -
1043B ASP 3.3 35.2 - - - +
1044B ALA* 3.7 9.2 - - + -
1050B ILE* 6.0 0.9 - - + -
1055B ILE* 3.9 27.3 - - + +
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Residues in contact with SER1032 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
803B LEU* 2.9 48.5 + - - +
804B GLY* 3.1 15.4 + - - -
822B ASN* 5.0 0.2 + - - -
1028B GLU* 2.9 27.7 + - - +
1029B CYS 2.8 5.5 + - - -
1031B LEU* 1.3 71.6 - - - +
1033B LYS* 1.3 59.6 + - - +
1035B ALA* 3.9 4.5 - - - -
1036B ALA* 3.1 19.9 + - - +
1089B PRO* 3.2 16.0 - - - +
1090B THR* 5.0 1.1 - - - -
1091B TYR 5.5 0.5 + - - -
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Residues in contact with LYS1033 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1029B CYS 2.7 20.4 + - - +
1030B LEU* 3.7 8.1 - - + +
1032B SER* 1.3 70.5 - - - +
1034B VAL* 1.3 69.2 + - - +
1036B ALA* 3.5 3.9 + - - +
1037B LEU* 3.3 21.9 + - + +
1059B LEU* 3.5 28.3 - - + -
1064B TYR* 4.5 11.8 - - - +
1068B GLY* 3.1 26.0 + - - -
1070B GLU* 2.4 32.2 + - - +
1087B PHE 3.2 24.2 + - - +
1088B GLY* 4.1 0.9 - - - -
1089B PRO* 3.5 20.1 - - + +
44J TYR* 3.6 20.9 - - + +
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Residues in contact with VAL1034 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1030B LEU 3.4 7.8 + - - +
1031B LEU* 3.1 13.3 + - + +
1033B LYS* 1.3 74.8 - - - +
1035B ALA* 1.3 56.0 + - - +
1036B ALA 2.7 3.8 + - - -
1037B LEU* 2.6 35.7 + - + +
1038B SER* 2.8 25.4 + - - +
1055B ILE* 4.0 13.2 - - + +
1058B LEU* 4.2 23.3 - - + -
1059B LEU* 3.6 44.9 - - + +
1062B HIS* 5.0 4.0 - - + -
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Residues in contact with ALA1035 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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803B LEU* 4.0 11.4 - - + +
1031B LEU* 3.0 13.5 + - + +
1032B SER* 3.9 9.9 - - - +
1034B VAL* 1.3 79.3 - - - +
1036B ALA* 1.3 57.3 + - - +
1038B SER* 3.4 11.9 - - - -
1039B GLY* 2.9 26.3 + - - -
1040B ASN 3.2 19.6 + - - +
1041B GLU* 4.9 0.4 - - - -
1042B GLY* 3.8 18.8 - - - +
51J LEU* 3.4 6.4 - - - +
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Residues in contact with ALA1036 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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803B LEU* 3.9 16.6 - - + -
1032B SER 3.1 18.2 + - - +
1033B LYS* 3.6 7.9 - - - +
1034B VAL 2.7 5.7 + - - -
1035B ALA* 1.3 76.8 - - - +
1037B LEU* 1.3 61.6 + - - +
1039B GLY 3.7 4.2 + - - -
1089B PRO* 4.5 2.5 - - + -
44J TYR* 3.6 24.7 - - + -
47J ARG* 3.3 22.9 + - - +
48J ARG* 4.6 8.7 - - + +
51J LEU* 3.9 8.8 - - - +
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Residues in contact with LEU1037 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1033B LYS* 3.3 20.0 - - + +
1034B VAL* 2.6 12.6 + - - +
1036B ALA* 1.3 74.6 - - - +
1038B SER* 1.3 60.0 + - - +
1059B LEU* 4.1 13.2 - - + -
1062B HIS* 3.5 39.6 - - + +
1064B TYR* 3.3 48.0 - - + +
33J GLY* 4.6 1.7 - - - -
42J LYS 5.4 2.5 - - - +
44J TYR* 4.4 13.9 - - + +
47J ARG* 3.4 36.1 + - - +
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Residues in contact with SER1038 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1034B VAL* 2.8 20.2 + - - +
1035B ALA* 3.4 16.6 + - - -
1037B LEU* 1.3 73.6 - - - +
1039B GLY* 1.3 63.9 + - - +
1040B ASN* 3.1 38.3 + - - +
1062B HIS* 4.1 16.6 - - - -
31J ASP* 5.3 0.7 - - - +
33J GLY* 3.3 16.5 - - - -
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Residues in contact with GLY1039 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1035B ALA 2.9 13.4 + - - -
1036B ALA 3.7 1.9 + - - -
1037B LEU 3.3 3.8 + - - -
1038B SER* 1.3 77.5 - - - +
1040B ASN* 1.3 61.3 + - - +
1041B GLU 4.1 1.1 + - - -
32J GLU* 3.2 28.7 - - - +
33J GLY* 3.9 12.7 + - - -
36J LEU* 4.9 3.1 - - - -
51J LEU* 3.7 25.0 - - - +
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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
------------------------------------------------------------
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