Contacts of the helix formed by residues 1023 - 1034 (chain A) in PDB entry 6SA5
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 ASP1023 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1021A SER 4.1 2.2 - - - +
1022A TRP* 1.3 75.2 + - - +
1024A THR* 1.3 65.4 + - - +
1025A ASN* 3.3 19.1 + - - +
1026A ASP* 3.1 30.7 + - - +
1027A ALA 3.0 17.2 + - - -
1042A ALA* 3.5 13.5 - - - +
1061A ARG* 6.0 0.3 - - - -
1062A CYS 5.0 1.0 - - - +
1204A MG 3.7 11.9 - - - -
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Residues in contact with THR1024 (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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1023A ASP* 1.3 73.7 - - - +
1025A ASN* 1.3 64.8 + - - +
1027A ALA* 3.8 3.4 - - + +
1028A ASN* 2.9 40.7 + - - -
1039A ALA* 5.0 8.7 - - - +
1040A MET 5.2 1.3 - - - +
1041A SER* 4.6 10.1 - - - +
1042A ALA* 4.1 23.6 - - + +
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Residues in contact with ASN1025 (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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1023A ASP* 3.2 17.4 + - - +
1024A THR* 1.3 81.7 + - - +
1026A ASP* 1.3 62.3 + - - +
1028A ASN* 3.4 7.6 + - - +
1029A VAL* 3.4 18.0 + - - +
1062A CYS* 3.5 22.7 + - - +
1063A SER* 3.5 21.1 + - - +
1064A GLY* 3.6 20.0 - - - -
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Residues in contact with ASP1026 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1021A SER 3.3 5.2 - - - +
1022A TRP* 3.4 32.7 - - + -
1023A ASP* 3.1 18.6 + - - +
1025A ASN* 1.3 75.8 - - - +
1027A ALA* 1.3 61.8 + - - +
1029A VAL* 3.2 6.2 + - - +
1030A VAL* 3.2 22.9 + - - +
1060A VAL* 3.0 11.1 - - - +
1062A CYS* 2.9 40.9 + - - -
1069A LEU* 4.2 1.6 - - + +
1204A MG 2.4 26.7 - - - -
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Residues in contact with ALA1027 (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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1022A TRP* 4.3 1.9 - - - +
1023A ASP 3.0 5.5 + - - -
1024A THR* 3.8 4.7 - - - +
1025A ASN 3.3 0.2 - - - -
1026A ASP* 1.3 76.5 - - - +
1028A ASN* 1.3 58.0 + - - +
1030A VAL* 3.2 2.7 + - - +
1031A CYS* 2.9 32.9 + - - -
1039A ALA* 3.6 18.6 - - + -
1041A SER 4.0 4.0 - - - +
1042A ALA* 3.8 24.7 - - + -
1090A VAL* 3.8 27.8 - - + -
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Residues in contact with ASN1028 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1024A THR* 2.9 30.0 + - - +
1025A ASN* 3.7 12.4 + - - +
1026A ASP 3.3 0.4 - - - -
1027A ALA* 1.3 76.3 - - - +
1029A VAL* 1.3 62.3 + - - +
1031A CYS* 3.9 1.9 - - - +
1032A ARG* 3.1 33.5 + - - +
1037A GLY 4.8 1.6 - - - +
1038A TRP* 3.8 10.9 - - - +
1039A ALA* 2.9 35.9 + - - +
1064A GLY* 4.2 13.0 - - - +
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Residues in contact with VAL1029 (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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1025A ASN 3.4 13.2 + - - +
1026A ASP 3.2 8.6 + - - +
1028A ASN* 1.3 74.1 - - - +
1030A VAL* 1.3 65.3 + - - +
1032A ARG* 3.4 8.8 + - - +
1033A GLN* 2.9 23.0 + - - +
1062A CYS* 3.9 9.6 - - + -
1064A GLY 3.8 10.8 - - - -
1066A GLU* 3.4 44.7 - - - +
1067A SER 4.9 0.2 - - - +
1068A TYR 3.6 33.7 - - - +
1069A LEU* 3.7 10.5 - - + +
1072A CYS* 4.2 2.5 - - - -
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Residues in contact with VAL1030 (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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993A LEU* 4.0 27.4 - - + -
995A LEU* 4.0 13.9 - - + -
1006A VAL* 4.6 3.4 - - + -
1022A TRP* 3.9 23.8 - - + -
1026A ASP 3.2 13.6 + - - +
1027A ALA 3.2 6.7 + - - +
1029A VAL* 1.3 75.3 - - - +
1031A CYS* 1.3 62.8 + - - +
1033A GLN* 3.2 8.8 + - - +
1034A LEU* 3.1 33.1 + - + +
1069A LEU* 4.0 20.6 - - + -
1090A VAL* 4.1 16.4 - - + -
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Residues in contact with CYS1031 (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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1027A ALA 2.9 21.8 + - - +
1028A ASN 3.9 2.7 - - - +
1030A VAL* 1.3 75.4 - - - +
1032A ARG* 1.3 61.7 + - - +
1034A LEU* 3.4 0.6 + - - -
1035A GLY 3.3 2.8 + - - -
1036A CYS* 2.8 29.9 + - - +
1037A GLY 3.4 19.5 - - - +
1038A TRP 4.2 2.5 - - - -
1039A ALA* 3.8 16.4 - - - +
1090A VAL* 4.5 6.5 - - - -
1091A ILE 4.5 0.7 - - - -
1092A CYS* 2.1 59.0 - - + -
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Residues in contact with ARG1032 (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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1028A ASN* 3.1 30.1 + - - +
1029A VAL* 3.7 4.7 - - - +
1031A CYS* 1.3 75.0 - - - +
1033A GLN* 1.3 65.3 + - - +
1035A GLY* 3.1 12.9 + - - -
1036A CYS 5.0 0.7 - - - +
1037A GLY 3.8 8.8 + - - +
1064A GLY 3.1 27.7 + - - -
1065A HIS* 3.7 15.2 + - - +
1066A GLU 3.2 25.3 + - - +
1067A SER* 5.0 9.9 - - - +
1201A SO4 3.0 41.8 + - - +
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Residues in contact with GLN1033 (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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993A LEU* 3.9 19.5 - - + +
1029A VAL 2.9 18.3 + - - +
1030A VAL* 3.6 5.3 - - - +
1032A ARG* 1.3 76.1 - - - +
1034A LEU* 1.3 64.1 + - + +
1035A GLY 3.6 0.3 + - - -
1067A SER 3.7 17.6 + - - +
1068A TYR* 3.5 19.7 - - + +
1069A LEU* 3.0 29.6 + - - +
1070A TRP* 3.2 40.8 - - - -
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Residues in contact with LEU1034 (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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993A LEU* 3.7 43.1 - - + +
994A ARG* 4.9 2.0 - - - -
995A LEU* 3.6 39.3 - - + +
1001A ARG* 2.8 35.5 + - - +
1030A VAL* 3.1 19.7 + - + +
1031A CYS* 3.4 2.4 + - - +
1032A ARG 3.1 0.2 - - - -
1033A GLN* 1.3 81.2 - - + +
1035A GLY* 1.3 58.2 + - - +
1036A CYS* 3.8 14.6 - - + -
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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