Contacts of the helix formed by residues 1059 - 1067 (chain A) in PDB entry 2G15
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 ASN1059 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1058A LEU* 1.3 74.4 - - - +
1060A PRO* 1.3 79.7 - - - +
1061A GLU* 3.3 35.9 + - - +
1062A LEU* 3.0 30.0 + - + +
1063A VAL* 3.1 11.8 + - - +
1122A SER* 6.2 0.2 - - - -
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Residues in contact with PRO1060 (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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1047A LEU* 5.9 0.5 - - - +
1056A SER 6.0 0.2 - - - +
1058A LEU 3.3 8.7 - - - +
1059A ASN* 1.3 94.3 - - - +
1061A GLU* 1.3 62.5 + - + +
1063A VAL* 3.4 9.4 + - + +
1064A GLN* 3.1 35.5 + - - +
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Residues in contact with GLU1061 (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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1059A ASN* 3.1 23.9 - - - +
1060A PRO* 1.3 75.9 - - + +
1062A LEU* 1.3 66.2 + - - +
1064A GLN* 3.4 19.1 - - - +
1065A ALA* 3.1 24.1 + - - +
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Residues in contact with LEU1062 (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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1058A LEU* 4.3 17.9 - - + -
1059A ASN* 3.0 23.3 + - + +
1061A GLU* 1.3 79.3 - - - +
1063A VAL* 1.3 64.0 + - - +
1065A ALA* 3.0 15.1 + - - +
1066A VAL* 3.0 25.6 + - + +
1122A SER* 3.9 37.5 - - - +
1125A LEU* 4.6 3.4 - - + -
1126A THR* 3.6 24.0 - - + +
1129A ILE* 3.4 28.7 - - + -
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Residues in contact with VAL1063 (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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1047A LEU* 3.5 28.9 - - + -
1050A THR* 3.9 12.6 - - - +
1055A LEU* 3.9 43.3 - - + +
1058A LEU* 3.9 15.5 - - + +
1059A ASN 3.1 14.9 + - - +
1060A PRO* 3.8 10.3 - - + +
1061A GLU 3.4 0.2 - - - -
1062A LEU* 1.3 77.0 - - - +
1064A GLN* 1.3 57.3 + - - +
1066A VAL* 3.0 21.4 - - + +
1067A GLN* 2.8 18.5 + - - -
1125A LEU* 5.6 0.9 - - + -
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Residues in contact with GLN1064 (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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1046A LEU* 4.0 36.1 - - - +
1047A LEU* 5.1 3.7 - - + +
1060A PRO* 3.1 24.7 + - - +
1061A GLU* 3.4 24.8 + - - +
1063A VAL* 1.3 76.7 - - - +
1065A ALA* 1.3 62.4 + - - +
1066A VAL 3.2 0.2 - - - -
1067A GLN* 3.2 26.4 - - + +
1068A HIS* 4.7 1.0 + - - -
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Residues in contact with ALA1065 (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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1061A GLU 3.1 19.0 + - - +
1062A LEU* 3.0 9.4 + - - +
1064A GLN* 1.3 79.5 - - - +
1066A VAL* 1.3 52.7 + - - +
1068A HIS* 2.7 38.4 + - + -
1129A ILE* 3.6 20.5 - - + +
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Residues in contact with VAL1066 (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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1050A THR* 4.6 13.5 - - + -
1055A LEU* 5.3 0.4 - - + -
1062A LEU* 3.0 10.5 + - + +
1063A VAL* 3.0 26.7 - - + +
1065A ALA* 1.3 73.5 - - - +
1067A GLN* 1.3 71.2 + - - +
1068A HIS 3.2 3.1 - - - -
1069A VAL* 2.8 23.7 + - + +
1070A VAL* 3.4 12.4 + - + +
1125A LEU* 3.6 42.0 - - + +
1129A ILE* 3.1 31.6 - - + -
1145A ILE* 5.5 2.2 - - + -
1147A LEU* 5.7 0.7 - - + -
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Residues in contact with GLN1067 (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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1046A LEU 4.4 4.0 + - - +
1047A LEU* 4.0 14.4 - - - +
1048A GLN* 3.7 10.5 + - + +
1049A ASN* 2.7 63.7 + - - +
1050A THR* 2.9 30.4 + - - +
1063A VAL* 2.8 31.5 + - - +
1064A GLN* 3.2 18.4 + - - +
1065A ALA 3.3 0.2 - - - -
1066A VAL* 1.3 82.4 - - - +
1068A HIS* 1.3 62.9 + - - +
1069A VAL 3.2 1.2 + - - -
1070A VAL* 3.2 11.4 + - - +
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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