Contacts of the helix formed by residues 1029 - 1041 (chain A) in PDB entry 3F2B
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 ARG1029 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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236A LEU* 3.2 24.2 + - - +
239A ILE* 2.9 30.5 + - - +
276A ASN* 3.0 17.4 + - - +
277A SER 2.8 32.1 + - - +
278A ILE* 3.5 29.2 - - - +
279A LEU 5.6 0.4 - - - +
316A ASP* 3.6 18.6 - - - +
317A LEU* 4.2 27.1 - - + +
1027A GLU 4.2 0.4 + - - -
1028A LEU* 1.3 77.4 - - - +
1030A GLY* 1.3 67.3 + - - +
1031A ALA* 4.2 7.6 - - + +
1032A GLU* 3.1 12.1 + - + +
1033A ILE* 3.0 20.4 + - - +
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Residues in contact with GLY1030 (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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314A VAL* 6.5 0.4 - - - -
316A ASP* 2.9 19.7 + - - -
1028A LEU 3.7 2.0 + - - -
1029A ARG* 1.3 68.0 - - - +
1031A ALA* 1.3 56.1 + - - +
1033A ILE* 2.8 30.3 + - - +
1034A ASP* 2.9 21.8 + - - +
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Residues in contact with ALA1031 (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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253A PHE* 3.3 15.1 - - - -
270A LYS* 4.3 19.7 - - + +
277A SER* 3.8 3.2 - - - +
278A ILE* 3.8 35.9 - - - +
279A LEU* 3.8 9.0 - - + +
316A ASP* 4.8 0.4 + - - -
1029A ARG* 3.2 4.5 - - + +
1030A GLY* 1.3 73.9 - - - +
1032A GLU* 1.3 55.7 + - - +
1034A ASP* 3.6 11.6 + - - +
1035A ARG 3.2 18.9 + - - -
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Residues in contact with GLU1032 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275A THR 4.3 1.6 - - - +
276A ASN* 3.4 44.2 + - - +
277A SER* 2.7 31.4 + - - +
1028A LEU* 4.1 13.2 - - + -
1029A ARG* 3.1 17.4 + - + +
1031A ALA* 1.3 75.7 - - - +
1033A ILE* 1.3 65.7 + - - +
1034A ASP 3.3 0.2 - - - -
1035A ARG* 2.9 33.7 + - - +
1036A LEU* 3.2 36.8 + - + +
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Residues in contact with ILE1033 (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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1014A TYR* 3.7 25.8 - - + -
1017A VAL* 4.2 20.3 - - + +
1018A LYS* 4.7 25.1 - - + -
1021A ALA* 5.9 4.5 - - + -
1028A LEU* 4.0 31.0 - - + +
1029A ARG 3.0 17.3 + - - +
1030A GLY* 2.8 12.5 + - - +
1032A GLU* 1.3 74.5 - - - +
1034A ASP* 1.3 67.8 + - - +
1036A LEU* 3.8 2.6 - - - +
1037A ALA* 2.9 22.0 + - - +
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Residues in contact with ASP1034 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
253A PHE* 4.1 11.7 - - + -
270A LYS* 2.8 37.0 + - + +
1014A TYR* 2.7 36.9 + - - +
1030A GLY* 2.9 20.2 + - - +
1031A ALA* 3.6 9.3 - - - +
1032A GLU 3.3 0.2 - - - -
1033A ILE* 1.3 76.8 - - - +
1035A ARG* 1.3 58.5 + - - +
1037A ALA* 3.1 4.2 - - - +
1038A ALA* 2.9 27.7 + - - +
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Residues in contact with ARG1035 (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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253A PHE* 3.5 31.2 - - + -
272A THR* 3.6 19.2 + - + +
274A TYR* 3.5 34.7 + - - +
275A THR 4.5 4.8 + - - -
277A SER* 2.9 21.3 - - - +
750A GLU 5.3 1.2 + - - -
753A ILE* 4.2 13.1 - - - +
754A TYR* 2.7 44.5 + - - -
1031A ALA 3.2 4.4 + - - -
1032A GLU* 2.9 34.7 + - - +
1033A ILE 3.2 0.8 - - - -
1034A ASP* 1.3 77.3 - - - +
1036A LEU* 1.3 81.6 + - - +
1038A ALA* 3.2 8.1 + - + +
1039A GLY 3.2 16.8 + - - -
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Residues in contact with LEU1036 (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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753A ILE* 4.0 24.2 - - + -
754A TYR* 3.8 9.3 - - + -
757A ILE* 4.1 13.2 - - + -
1017A VAL* 3.8 24.0 - - + -
1020A TYR* 5.9 2.9 - - + -
1028A LEU* 3.9 26.2 - - + -
1032A GLU* 3.2 25.8 + - + +
1033A ILE 3.9 1.8 - - - +
1035A ARG* 1.3 104.8 - - - +
1037A ALA* 1.3 69.3 + - - +
1039A GLY* 3.1 9.4 + - - -
1040A CYS* 3.4 17.2 + - - -
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Residues in contact with ALA1037 (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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1010A ASP* 5.6 1.1 - - - +
1013A ALA* 3.5 24.5 - - + +
1014A TYR* 3.7 41.1 - - + +
1017A VAL* 3.7 10.6 - - + +
1033A ILE 2.9 14.5 + - - +
1034A ASP 3.1 10.3 - - - +
1036A LEU* 1.3 76.4 - - - +
1038A ALA* 1.3 63.5 + - - +
1039A GLY 3.0 1.6 + - - -
1040A CYS* 3.0 10.9 + - - +
1041A THR* 3.6 4.5 + - - +
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Residues in contact with ALA1038 (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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253A PHE* 5.7 6.7 - - + -
1010A ASP* 5.6 2.0 - - - -
1034A ASP 2.9 15.3 + - - +
1035A ARG* 3.2 9.1 + - - +
1037A ALA* 1.3 75.6 - - - +
1039A GLY* 1.3 57.2 + - - +
1041A THR* 3.2 24.6 + - - +
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Residues in contact with GLY1039 (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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357A VAL* 3.9 20.1 - - - +
754A TYR* 3.4 45.9 - - - +
1035A ARG 3.2 4.4 + - - -
1036A LEU 3.1 3.6 + - - -
1037A ALA 3.0 1.4 + - - -
1038A ALA* 1.3 78.2 - - - +
1040A CYS* 1.3 59.3 + - - +
1041A THR 3.6 2.5 - - - +
1043A VAL* 5.1 0.5 - - - +
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Residues in contact with CYS1040 (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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754A TYR* 4.1 24.2 - - - -
757A ILE* 4.2 21.5 - - - -
758A LEU* 4.5 18.4 - - + +
1008A VAL* 3.7 14.2 - - + +
1013A ALA* 4.2 13.9 - - + -
1016A PHE* 5.5 1.3 - - + -
1017A VAL* 4.5 5.6 - - - -
1036A LEU 3.4 16.2 - - - -
1037A ALA 3.0 7.5 + - - +
1039A GLY* 1.3 80.4 - - - +
1041A THR* 1.3 63.9 + - - +
1043A VAL* 3.4 20.8 - - - +
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Residues in contact with THR1041 (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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350A PRO* 5.8 0.7 - - - +
357A VAL 5.4 2.8 - - - +
1008A VAL* 3.2 15.5 - - - +
1009A ALA* 4.1 7.9 - - - -
1010A ASP* 3.9 21.8 - - - +
1013A ALA* 3.9 13.2 - - + -
1037A ALA 3.6 14.6 - - - +
1038A ALA* 3.2 16.8 + - - +
1039A GLY 3.6 2.8 - - - +
1040A CYS* 1.3 81.5 + - - +
1042A GLY* 1.3 60.6 + - - +
1043A VAL* 3.3 4.0 + - - +
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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
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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