Contacts of the helix formed by residues 1031 - 1037 (chain A) in PDB entry 3E0D
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 GLU1031 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1027A CYS* 2.3 45.6 - - - -
1028A THR* 1.9 64.5 + - + +
1030A GLU* 1.3 70.4 - - + +
1032A LEU* 1.3 52.0 + - - -
1033A SER 3.5 0.7 - - - -
1034A GLU* 3.3 24.3 + - - +
1035A PHE* 2.7 34.6 + - + +
1166A LEU* 5.7 2.4 - - - +
1171A GLU* 3.8 22.3 - - + +
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Residues in contact with LEU1032 (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 CYS* 3.6 6.5 - - + -
1028A THR 3.5 1.8 + - - -
1029A ILE 3.4 14.1 + - - +
1030A GLU 3.2 2.0 + - - -
1031A GLU* 1.3 76.0 - - - +
1033A SER* 1.3 54.9 + - - +
1035A PHE* 4.7 3.6 - - + -
1036A VAL* 2.8 61.2 + - + +
1045A VAL* 4.1 22.4 - - + -
1047A LEU* 3.9 20.6 - - + -
1077A LEU* 3.7 33.0 - - + -
1105A VAL* 4.5 8.7 - - + -
1113A VAL* 3.9 20.4 - - + -
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Residues in contact with SER1033 (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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1029A ILE 5.0 0.2 + - - -
1030A GLU 4.1 9.9 + - - -
1032A LEU* 1.3 76.4 - - - +
1034A GLU* 1.3 68.0 + - - +
1036A VAL* 5.0 2.2 - - - -
1037A ARG* 3.2 61.3 + - - +
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Residues in contact with GLU1034 (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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1030A GLU 5.2 0.9 - - - +
1031A GLU* 3.3 28.6 + - - +
1033A SER* 1.3 83.4 + - - +
1035A PHE* 1.3 60.5 + - - +
1037A ARG* 3.9 21.0 + - - +
1038A GLU* 4.9 3.5 + - - +
1168A PRO 5.2 0.3 - - - +
1169A PHE* 3.4 23.1 - - + +
1170A GLY* 2.8 48.4 + - - +
1171A GLU* 3.7 4.3 + - - +
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Residues in contact with PHE1035 (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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1026A SER 3.8 16.4 - - - -
1027A CYS* 3.8 15.9 - - + -
1031A GLU* 2.7 21.5 + - + +
1032A LEU* 3.9 2.0 - - + +
1034A GLU* 1.3 73.0 - - - +
1036A VAL* 1.3 75.6 + - + +
1038A GLU* 3.5 15.9 + - - +
1039A LEU* 4.4 24.1 - - + +
1045A VAL* 4.0 22.9 - - + -
1170A GLY* 4.5 0.2 - - - -
1171A GLU 2.2 44.9 - - - +
1172A ALA* 3.4 16.2 - - - -
1173A LEU* 3.5 30.5 - - + -
1202A ARG* 5.1 2.2 - - - -
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Residues in contact with VAL1036 (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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1032A LEU* 2.8 45.4 + - + +
1033A SER* 4.4 1.6 - - - +
1035A PHE* 1.3 78.3 - - + +
1037A ARG* 1.3 71.2 + - - +
1038A GLU 2.9 4.2 + - - -
1039A LEU* 3.2 28.6 - - + +
1040A PRO 5.1 0.5 - - - +
1043A PRO* 3.8 28.9 - - + +
1045A VAL* 4.5 10.8 - - + -
1105A VAL* 4.1 23.8 - - + +
1106A GLU 6.0 2.2 - - - -
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Residues in contact with ARG1037 (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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1033A SER* 3.2 42.1 + - - +
1034A GLU* 3.9 24.8 - - - +
1036A VAL* 1.3 81.3 - - - +
1038A GLU* 1.3 58.3 + - + +
1039A LEU 3.3 5.0 + - - +
1040A PRO 5.1 3.3 - - - +
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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