Contacts of the helix formed by residues 981 - 994 (chain B) in PDB entry 4HPF
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 981 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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980B ASN* 1.3 82.9 - - + +
982B PHE* 1.3 67.9 + - - +
984B GLN* 2.7 38.4 + - + +
985B LEU* 2.8 11.4 + - - +
1023B ASN 3.0 2.9 + - - +
1024B GLU* 3.0 16.9 - - + -
1025B PHE 3.0 27.5 + - - -
1026B LYS* 5.1 0.9 - - - -
1027B LEU* 3.6 4.5 - - - -
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Residues in contact with PHE 982 (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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547B PHE* 4.0 17.0 - + - -
553B LEU* 4.8 3.8 - - + -
981B THR* 1.3 72.1 + - - +
983B GLY* 1.3 54.4 + - - +
985B LEU* 3.0 5.7 + - + +
986B PHE* 2.7 38.6 + - + +
997B CYS* 3.8 35.9 - - + -
998B VAL* 4.5 5.8 - - - -
999B GLY 4.5 8.3 - - - -
1000B LEU* 4.2 19.1 - - + -
1020B ARG* 3.9 13.7 - - - -
1021B PRO* 3.4 44.0 - - + -
1022B ALA 3.6 24.5 - - - +
1023B ASN 3.8 0.2 - - - +
1025B PHE* 3.1 10.7 + - + -
1027B LEU* 3.3 21.7 - - + +
1033B VAL* 5.5 0.2 - - + -
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Residues in contact with GLY 983 (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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547B PHE* 3.5 27.1 - - - -
548B LEU* 6.1 0.7 - - - -
982B PHE* 1.3 73.4 - - - +
984B GLN* 1.3 61.8 + - - +
986B PHE* 3.5 0.7 + - - +
987B CYS* 3.2 32.0 + - - -
1023B ASN* 2.5 25.7 + - - -
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Residues in contact with GLN 984 (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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980B ASN* 4.6 7.2 - - + +
981B THR* 2.7 42.1 + - + +
983B GLY* 1.3 74.1 - - - +
985B LEU* 1.3 61.3 + - - +
987B CYS* 3.4 4.0 + - - +
988B GLY* 3.4 17.5 + - - -
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Residues in contact with LEU 985 (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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968B LEU* 3.8 28.9 - - + -
973B LEU* 4.0 33.4 - - + +
980B ASN 5.4 2.8 - - - +
981B THR 2.8 10.5 + - - +
982B PHE* 3.4 9.9 - - + +
984B GLN* 1.3 73.9 - - - +
986B PHE* 1.3 58.0 + - - +
987B CYS 3.2 0.2 + - - -
988B GLY* 4.2 0.4 - - - -
989B SER* 2.6 35.3 + - - +
997B CYS* 4.6 9.0 - - + -
1000B LEU* 5.5 0.9 - - + -
1027B LEU* 3.7 24.9 - - + -
1033B VAL* 4.2 21.3 - - + -
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Residues in contact with PHE 986 (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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543B ALA* 4.6 11.0 - - + -
544B ARG* 5.1 2.2 - - + -
547B PHE* 3.2 56.1 - + + -
553B LEU* 3.5 26.0 - - + -
554B LEU 5.5 0.7 - - - -
982B PHE* 2.7 26.5 + + + +
983B GLY 3.6 3.6 - - - +
985B LEU* 1.3 73.7 - - - +
987B CYS* 1.3 67.2 + - - +
989B SER* 2.9 16.9 + - - -
990B LEU* 3.3 33.9 + - + +
995B ILE 4.4 0.3 - - - +
996B LEU* 3.8 16.2 - - + -
997B CYS* 3.2 37.4 - - - +
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Residues in contact with CYS 987 (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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544B ARG* 4.6 20.3 - - - +
547B PHE* 4.4 0.4 - - - -
548B LEU* 3.9 38.1 - - - -
983B GLY 3.2 18.5 + - - +
984B GLN* 3.9 4.7 - - - +
985B LEU 3.2 0.2 - - - -
986B PHE* 1.3 91.7 - - - +
988B GLY* 1.3 66.9 + - - +
990B LEU* 3.3 4.8 + - - +
991B ASP* 2.9 27.5 + - - +
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Residues in contact with GLY 988 (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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984B GLN 3.4 11.0 + - - -
985B LEU* 4.2 0.9 - - - -
987B CYS* 1.3 79.0 - - - +
989B SER* 1.3 64.6 + - - +
991B ASP* 3.6 1.7 - - - -
992B LEU* 2.8 44.3 + - - +
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Residues in contact with SER 989 (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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973B LEU* 3.5 30.1 - - - -
985B LEU* 2.6 26.6 + - - +
986B PHE* 2.9 16.6 + - - -
988B GLY* 1.3 72.2 - - - +
990B LEU* 1.3 56.2 + - - +
993B PHE* 2.9 39.2 + - - +
994B GLY 3.3 4.3 + - - -
995B ILE* 3.3 20.5 + - - +
997B CYS* 3.6 8.8 - - - -
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Residues in contact with LEU 990 (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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539B PHE* 5.2 0.4 - - + -
540B PRO* 3.6 44.6 - - + +
543B ALA* 3.9 16.6 - - + -
544B ARG* 4.0 15.7 - - + +
573B ASN* 4.2 17.9 - - - +
986B PHE* 3.3 28.0 + - + +
987B CYS* 3.6 3.6 - - - +
988B GLY 3.1 0.8 - - - -
989B SER* 1.3 81.1 + - - +
991B ASP* 1.3 58.6 + - - +
992B LEU 3.0 2.2 + - - -
994B GLY* 2.7 36.7 + - - -
995B ILE 3.3 16.5 + - - +
996B LEU* 4.6 10.3 - - + -
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Residues in contact with ASP 991 (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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540B PRO* 5.6 5.2 - - + -
544B ARG* 4.7 22.4 - - + +
987B CYS 2.9 19.8 + - - +
988B GLY* 3.6 2.0 - - - +
990B LEU* 1.3 73.5 - - + +
992B LEU* 1.3 64.9 + - + +
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Residues in contact with LEU 992 (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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988B GLY* 2.8 29.1 + - - +
990B LEU 4.0 0.2 - - - -
991B ASP* 1.3 85.8 - - + +
993B PHE* 1.3 91.5 + - + +
994B GLY 3.7 0.7 - - - -
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Residues in contact with PHE 993 (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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972B ILE* 3.2 49.4 - - + -
973B LEU* 4.9 4.0 - - + -
989B SER* 2.9 24.0 + - - +
992B LEU* 1.3 106.2 - - + +
994B GLY* 1.3 65.7 + - - +
995B ILE* 3.4 18.6 + - + +
1038B PRO* 4.1 9.9 - - - +
1041B THR* 5.1 8.7 + - + +
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Residues in contact with GLY 994 (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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540B PRO* 5.8 4.7 - - - -
573B ASN* 2.9 25.0 + - - -
576B PRO* 6.2 4.0 - - - -
990B LEU* 2.7 34.2 + - - -
992B LEU 3.7 0.8 - - - -
993B PHE* 1.3 73.4 - - - +
995B ILE* 1.3 57.0 + - - +
1038B PRO* 3.5 12.6 - - - +
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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