Contacts of the helix formed by residues 1065 - 1079 (chain C) 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 C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1061C TYR* 4.5 6.4 - - + -
1062C ALA* 3.1 29.0 + - + +
1063C GLU 4.0 2.9 - - - +
1064C ASP* 1.3 76.7 - - - +
1066C ASN* 1.3 60.7 + - - +
1067C ILE* 3.2 26.7 - - - +
1068C TYR* 3.3 31.8 + - + +
1069C GLN* 3.4 17.8 + - - +
1238C ARG* 3.2 11.2 + - - -
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Residues in contact with ASN1066 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1063C GLU 3.9 13.1 + - - -
1064C ASP 3.3 11.3 + - - +
1065C ASP* 1.3 73.1 + - - +
1067C ILE* 1.3 61.9 - - - +
1069C GLN* 3.1 6.7 + - - +
1070C GLN* 2.9 31.9 + - - +
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Residues in contact with ILE1067 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1065C ASP* 3.2 19.1 - - - +
1066C ASN* 1.3 76.2 - - + +
1068C TYR* 1.3 55.8 + - - +
1070C GLN* 3.3 8.3 + - - +
1071C LYS* 2.9 37.1 + - + +
1237C ASP 5.2 0.2 - - - +
1238C ARG* 3.4 58.8 - - + +
1239C GLY 3.9 21.1 - - - +
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Residues in contact with TYR1068 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1061C TYR* 3.5 40.2 - + + -
1065C ASP* 3.3 28.9 + - + +
1066C ASN 3.4 0.4 - - - -
1067C ILE* 1.3 82.8 - - + +
1069C GLN* 1.3 57.6 + - - +
1071C LYS* 3.1 6.8 + - + +
1072C ILE* 2.9 33.7 + - - +
1236C MET* 3.5 33.9 - - + -
1237C ASP* 3.2 28.4 + - - -
1238C ARG* 3.4 24.0 - - - +
1262C ARG* 5.6 1.1 - - + -
1263C PRO* 3.9 24.8 - - + +
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Residues in contact with GLN1069 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1058C TYR* 3.2 51.0 + - + +
1061C TYR* 3.9 15.0 - - - +
1062C ALA 3.4 21.0 - - - +
1063C GLU* 4.8 12.1 + - - -
1065C ASP 3.4 15.7 + - - +
1066C ASN* 3.1 7.3 + - - +
1068C TYR* 1.3 78.4 - - - +
1070C GLN* 1.3 57.5 + - - +
1072C ILE* 3.1 12.5 + - - +
1073C LYS* 3.0 34.9 + - - +
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Residues in contact with GLN1070 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1066C ASN 2.9 16.8 + - - +
1067C ILE* 3.6 9.6 - - - +
1069C GLN* 1.3 72.9 - - - +
1071C LYS* 1.3 65.6 + - - +
1072C ILE 3.1 1.1 - - - -
1073C LYS* 3.1 24.2 + - + +
1074C ASP* 2.9 24.7 + - - +
1241C GLY* 4.2 2.0 - - - +
1242C GLY* 3.1 37.5 - - - +
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Residues in contact with LYS1071 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1067C ILE* 2.9 22.1 + - + +
1068C TYR* 3.1 9.6 + - - +
1070C GLN* 1.3 82.6 - - - +
1072C ILE* 1.3 57.7 + - - +
1074C ASP* 3.4 2.3 + - - +
1075C LEU* 2.9 27.2 + - - +
1235C TYR 4.9 0.4 - - - -
1236C MET* 4.2 12.9 - - + +
1237C ASP* 4.0 33.8 + - - +
1238C ARG* 4.1 1.1 - - - -
1239C GLY* 3.3 37.1 - - - +
1241C GLY 4.6 0.7 - - - +
1242C GLY* 3.3 19.5 + - - +
1243C THR 2.6 30.3 + - - -
1244C THR* 3.6 20.1 - - + +
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Residues in contact with ILE1072 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1054C LEU* 4.7 5.3 - - + +
1057C LEU* 3.6 49.4 - - + +
1058C TYR* 3.7 31.6 - - + +
1061C TYR* 3.8 22.2 - - + -
1068C TYR 2.9 18.6 + - - +
1069C GLN* 3.2 16.8 - - - +
1071C LYS* 1.3 75.8 - - - +
1073C LYS* 1.3 57.8 + - - +
1075C LEU* 3.3 7.5 + - + +
1076C HIS* 2.9 28.0 + - + +
1236C MET* 3.7 16.4 - - + -
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Residues in contact with LYS1073 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1058C TYR* 3.6 22.1 - - + +
1069C GLN* 3.0 27.4 + - - +
1070C GLN* 3.1 25.1 - - + +
1072C ILE* 1.3 77.2 - - - +
1074C ASP* 1.3 55.9 + - - +
1076C HIS* 2.9 19.6 + - - +
1077C LYS* 3.0 19.7 + - + +
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Residues in contact with ASP1074 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1070C GLN 2.9 10.2 + - - +
1071C LYS 3.6 3.8 - - - +
1073C LYS* 1.3 76.2 - - - +
1075C LEU* 1.3 61.3 + - - +
1077C LYS* 3.2 32.5 + - - +
1078C LYS* 3.5 21.5 + - - +
1242C GLY* 3.1 31.1 - - - +
1243C THR* 3.7 14.5 + - - +
1244C THR* 3.2 25.3 + - - -
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Residues in contact with LEU1075 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1054C LEU* 4.0 11.8 - - + +
1057C LEU* 4.3 16.6 - - + -
1071C LYS 2.9 16.8 + - - +
1072C ILE* 3.7 7.9 - - + +
1073C LYS 3.2 0.2 - - - -
1074C ASP* 1.3 77.2 + - - +
1076C HIS* 1.3 58.1 + - - +
1078C LYS* 3.4 2.0 + - + +
1079C TYR* 3.0 38.2 + - + +
1234C GLU* 4.2 12.1 - - + -
1236C MET* 4.3 7.9 - - - -
1244C THR* 3.7 22.4 - - + +
1260C LEU* 3.8 35.2 - - + -
1269C LEU* 4.0 25.1 - - + -
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Residues in contact with HIS1076 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1053C GLU* 4.2 10.8 - - - -
1054C LEU* 3.3 31.6 - - + +
1055C SER* 3.9 17.6 + - - -
1058C TYR* 3.5 34.0 - + - +
1072C ILE* 2.9 13.5 + - + +
1073C LYS* 2.9 12.8 + - - +
1075C LEU* 1.3 74.6 - - - +
1077C LYS* 1.3 65.7 + - + +
1078C LYS 3.4 0.2 - - - -
1079C TYR 3.5 13.4 + - - +
1080C SER* 4.9 2.7 - - - -
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Residues in contact with LYS1077 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1073C LYS* 3.0 16.7 + - + +
1074C ASP* 3.2 25.3 + - - +
1076C HIS* 1.3 81.0 - - - +
1078C LYS* 1.3 64.0 + - + +
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Residues in contact with LYS1078 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1074C ASP* 3.5 32.5 + - - +
1075C LEU* 3.4 2.7 + - - +
1076C HIS 3.4 0.2 - - - -
1077C LYS* 1.3 83.0 - - + +
1079C TYR* 1.3 79.8 + - + +
1080C SER 4.4 0.3 + - - -
1234C GLU* 3.7 19.7 + - - +
1243C THR* 5.1 3.4 - - - +
1244C THR* 2.6 33.3 + - - +
1245C ASN* 4.8 0.2 - - - +
1246C PRO* 4.3 10.2 - - + +
1271C LYS* 3.9 21.0 - - - +
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Residues in contact with TYR1079 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1054C LEU* 3.3 28.2 - - + +
1075C LEU* 3.0 17.6 + - + +
1076C HIS* 3.5 14.3 + - - +
1077C LYS 3.7 0.2 - - - -
1078C LYS* 1.3 96.7 - - + +
1080C SER* 1.3 60.2 + - - +
1081C TYR 4.6 3.6 - - - +
1232C GLN* 2.8 29.8 + - - +
1234C GLU* 3.1 36.3 + - + +
1258C TYR* 3.9 23.2 - + + +
1269C LEU* 3.6 27.6 - - + -
1270C TYR 3.8 6.5 - - - +
1271C LYS* 3.5 35.2 - - + +
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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
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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