Contacts of the helix formed by residues 1065 - 1079 (chain B) in PDB entry 4DDG
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 ASP1065 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1061B TYR* 4.5 6.9 - - + -
1062B ALA* 3.1 28.3 + - + +
1063B GLU 4.0 2.5 - - - +
1064B ASP* 1.3 76.9 - - - +
1066B ASN* 1.3 61.7 + - - +
1067B ILE* 3.2 27.4 - - - +
1068B TYR* 3.3 32.0 + - + +
1069B GLN* 3.4 16.8 + - - +
1238B ARG* 3.2 10.6 + - - -
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Residues in contact with ASN1066 (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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1063B GLU 3.9 13.1 + - - -
1064B ASP 3.3 11.2 + - - +
1065B ASP* 1.3 73.7 + - - +
1067B ILE* 1.3 61.7 + - + +
1069B GLN* 3.1 6.5 + - - +
1070B GLN* 2.9 32.0 + - - +
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Residues in contact with ILE1067 (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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1065B ASP* 3.2 18.6 - - - +
1066B ASN* 1.3 76.6 - - - +
1068B TYR* 1.3 56.1 + - - +
1070B GLN* 3.4 7.3 + - - +
1071B LYS* 2.9 36.7 + - + +
1238B ARG* 3.5 58.1 - - + +
1239B GLY 3.9 21.5 - - - +
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Residues in contact with TYR1068 (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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1061B TYR* 3.5 39.9 - + + -
1065B ASP* 3.3 28.9 + - + +
1066B ASN 3.4 0.2 - - - -
1067B ILE* 1.3 82.4 - - - +
1069B GLN* 1.3 58.4 + - - +
1071B LYS* 3.1 6.9 + - + +
1072B ILE* 2.9 33.7 + - - +
1236B MET* 3.5 34.3 - - + -
1237B ASP* 3.2 29.2 + - - -
1238B ARG* 3.4 24.6 - - + +
1262B ARG* 5.6 0.9 - - + -
1263B PRO* 3.9 24.6 - - + +
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Residues in contact with GLN1069 (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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1058B TYR* 3.2 51.0 + - + +
1061B TYR* 3.9 14.8 - - - +
1062B ALA 3.4 22.0 - - - +
1063B GLU* 4.8 11.0 + - - -
1065B ASP 3.4 14.8 + - - +
1066B ASN* 3.1 7.2 + - - +
1068B TYR* 1.3 78.3 - - - +
1070B GLN* 1.3 57.9 + - - +
1072B ILE* 3.1 12.8 + - - +
1073B LYS* 3.0 35.6 + - - +
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Residues in contact with GLN1070 (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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1066B ASN 2.9 16.4 + - - +
1067B ILE* 3.6 9.8 - - - +
1069B GLN* 1.3 73.7 - - - +
1071B LYS* 1.3 64.4 + - - +
1072B ILE 3.1 1.3 - - - -
1073B LYS* 3.1 23.5 + - + +
1074B ASP* 2.9 23.9 + - - +
1241B GLY 4.2 2.4 - - - +
1242B GLY* 3.1 37.6 - - - +
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Residues in contact with LYS1071 (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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1067B ILE* 2.9 22.5 + - + +
1068B TYR* 3.1 9.8 + - - +
1070B GLN* 1.3 82.4 - - - +
1072B ILE* 1.3 58.3 + - - +
1074B ASP* 3.4 2.4 + - - +
1075B LEU* 2.9 27.0 + - - +
1235B TYR 4.9 0.4 - - - -
1236B MET* 4.2 12.4 - - + +
1237B ASP* 4.0 34.5 + - - +
1238B ARG* 4.1 0.9 - - - -
1239B GLY* 3.3 37.6 - - - +
1241B GLY 4.6 0.9 - - - +
1242B GLY* 3.3 18.4 + - - +
1243B THR 2.6 30.7 + - - -
1244B THR* 3.6 20.3 - - + +
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Residues in contact with ILE1072 (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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1054B LEU* 4.7 5.3 - - + +
1057B LEU* 3.6 48.7 - - + +
1058B TYR* 3.7 30.7 - - + +
1061B TYR* 3.8 22.7 - - + -
1068B TYR 2.9 18.4 + - - +
1069B GLN* 3.2 17.0 - - - +
1071B LYS* 1.3 76.4 - - - +
1073B LYS* 1.3 58.0 + - - +
1075B LEU* 3.7 6.4 - - + +
1076B HIS* 2.9 28.3 + - + +
1236B MET* 3.7 16.4 - - + -
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Residues in contact with LYS1073 (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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1058B TYR* 3.6 23.5 - - + +
1069B GLN* 3.0 27.0 + - - +
1070B GLN* 3.1 26.4 + - + +
1072B ILE* 1.3 76.3 - - - +
1074B ASP* 1.3 56.8 + - - +
1076B HIS* 2.9 19.6 + - - +
1077B LYS* 3.0 20.5 + - + +
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Residues in contact with ASP1074 (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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1070B GLN 2.9 9.6 + - - +
1071B LYS 3.6 4.0 - - - +
1072B ILE 3.3 0.2 - - - -
1073B LYS* 1.3 77.3 - - - +
1075B LEU* 1.3 61.4 + - - +
1077B LYS* 3.2 30.8 + - - +
1078B LYS* 3.5 21.8 + - - +
1242B GLY* 3.1 31.3 - - - +
1243B THR* 3.7 14.2 + - - +
1244B THR* 3.2 26.3 + - - -
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Residues in contact with LEU1075 (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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1054B LEU* 4.0 10.5 - - + +
1057B LEU* 4.3 16.2 - - + -
1071B LYS 2.9 17.0 + - - +
1072B ILE* 3.7 8.1 - - + +
1073B LYS 3.2 0.2 - - - -
1074B ASP* 1.3 77.6 + - - +
1076B HIS* 1.3 58.8 + - - +
1078B LYS* 3.4 2.4 + - + +
1079B TYR* 3.0 40.0 + - + +
1234B GLU* 4.2 12.1 - - + -
1236B MET* 4.3 7.9 - - - -
1244B THR* 3.7 22.2 - - + +
1260B LEU* 3.8 35.2 - - + -
1269B LEU* 4.0 25.6 - - + -
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Residues in contact with HIS1076 (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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1053B GLU* 4.2 10.8 - - - -
1054B LEU* 3.3 32.3 - - + +
1055B SER* 3.9 16.5 + - - -
1058B TYR* 3.5 33.1 - + - +
1072B ILE* 2.9 12.9 + - + +
1073B LYS* 2.9 12.1 + - - +
1075B LEU* 1.3 75.4 - - - +
1077B LYS* 1.3 66.3 + - + +
1079B TYR 3.5 13.8 + - - +
1080B SER* 4.9 2.8 - - - -
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Residues in contact with LYS1077 (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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1073B LYS* 3.0 16.5 + - + +
1074B ASP* 3.2 24.8 + - + +
1076B HIS* 1.3 80.5 - - - +
1078B LYS* 1.3 64.0 + - + +
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Residues in contact with LYS1078 (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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1074B ASP* 3.5 30.8 + - - +
1075B LEU* 3.4 2.9 + - - +
1077B LYS* 1.3 83.0 - - + +
1079B TYR* 1.3 80.0 + - + +
1080B SER 4.4 0.5 + - - -
1234B GLU* 3.7 19.0 + - - +
1243B THR* 5.1 3.0 - - - +
1244B THR* 2.6 33.9 + - - +
1245B ASN* 4.8 0.2 - - - +
1246B PRO* 4.3 9.8 - - + +
1271B LYS* 3.9 20.8 - - - +
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Residues in contact with TYR1079 (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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1054B LEU* 3.3 28.6 - - + +
1075B LEU* 3.0 17.9 + - + +
1076B HIS* 3.5 14.8 + - - +
1077B LYS 3.7 0.2 - - - -
1078B LYS* 1.3 98.0 - - + +
1080B SER* 1.3 61.0 + - - +
1081B TYR 4.6 2.7 - - - +
1232B GLN* 2.8 30.1 + - - +
1234B GLU* 3.1 35.4 + - + +
1258B TYR* 3.9 23.4 - + + +
1269B LEU* 3.6 29.2 - - + -
1270B TYR 3.8 7.0 - - - +
1271B LYS* 3.5 34.8 - - + +
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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