Contacts of the helix formed by residues 1069 - 1075 (chain E) in PDB entry 3EI4
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 GLU1069 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1059E ASN* 6.2 2.2 - - + +
1067E LYS 3.6 5.2 + - - +
1068E ILE* 1.3 74.1 - - - +
1070E HIS* 1.3 68.0 + - - +
1071E SER* 3.7 17.4 + - - +
1072E PHE* 2.9 27.0 + - + +
1073E TRP 3.1 9.7 + - - -
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Residues in contact with HIS1070 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58E TYR* 3.7 47.2 - + + -
998E PHE* 5.9 0.2 - + - -
1055E GLN* 3.7 14.6 - - - -
1059E ASN* 3.8 22.7 + - - +
1068E ILE 3.4 4.2 + - - -
1069E GLU* 1.3 71.8 - - - +
1071E SER* 1.3 69.3 + - - +
1073E TRP* 2.9 18.2 + + - +
1074E ARG* 2.9 34.5 + - + +
1090E ASP* 3.3 26.2 + - - -
1093E LEU* 3.4 30.7 - - + +
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Residues in contact with SER1071 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1056E ASN* 6.1 1.1 - - - -
1059E ASN* 4.5 10.0 + - - +
1069E GLU* 3.7 22.7 + - - +
1070E HIS* 1.3 84.3 + - - +
1072E PHE* 1.3 60.8 + - - +
1074E ARG* 3.6 2.9 + - - +
1075E SER* 3.0 25.1 + - - -
1084E PRO 4.1 4.6 - - - +
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Residues in contact with PHE1072 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83E LYS* 3.0 42.3 + - + -
85E ASN* 3.3 35.9 - - - -
107E ASN* 3.3 22.4 - - - -
109E GLN* 4.8 7.2 - - - -
1068E ILE* 4.4 5.2 - - + -
1069E GLU* 2.9 23.4 + - + +
1071E SER* 1.3 76.4 + - - +
1073E TRP* 1.3 80.2 + - - +
1075E SER* 2.8 28.2 + - - -
1077E HIS* 6.3 0.2 - - - -
1082E THR* 5.4 10.1 - - + -
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Residues in contact with TRP1073 (chain E).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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37E THR* 3.8 23.1 - - + -
57E MET 4.7 1.2 + - - -
58E TYR* 3.4 53.0 - + + +
59E GLY* 3.3 37.0 - - - -
60E LYS* 3.8 6.3 - - + -
81E THR* 5.3 0.2 - - + -
83E LYS* 2.6 30.4 + - + +
85E ASN* 5.9 0.2 - - - -
999E HIS* 3.1 32.3 + + - -
1000E LEU 3.8 18.6 - - - -
1001E GLY* 4.1 6.5 - - - -
1068E ILE* 4.2 1.1 - - + -
1069E GLU 3.1 7.9 + - - +
1070E HIS* 2.9 13.5 + + - +
1072E PHE* 1.3 79.5 - - - +
1074E ARG* 1.3 94.6 + - + +
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Residues in contact with ARG1074 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37E THR* 6.0 0.2 - - - +
998E PHE* 3.3 39.3 - - + -
999E HIS* 2.7 51.1 + - - +
1000E LEU* 2.7 31.6 + - - +
1070E HIS* 2.9 37.1 + - + +
1071E SER* 4.2 3.6 - - - +
1073E TRP* 1.3 110.0 - - + +
1075E SER* 1.3 65.0 + - - +
1076E PHE 3.3 0.3 + - - -
1084E PRO 5.4 0.2 - - - +
1085E ALA* 3.8 7.8 - - + +
1090E ASP* 3.2 22.6 + - - +
1092E ASP* 5.4 7.7 + - - +
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Residues in contact with SER1075 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83E LYS* 2.9 22.9 + - - -
999E HIS* 3.5 1.4 - - - +
1071E SER 3.0 17.7 + - - -
1072E PHE* 2.8 23.1 + - - -
1074E ARG* 1.3 76.6 - - - +
1076E PHE* 1.3 64.3 + - - +
1077E HIS* 3.4 1.4 + - - +
1082E THR* 3.8 17.7 - - - +
1083E GLU 3.2 13.2 - - - -
1084E PRO* 3.3 23.8 - - - -
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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