Contacts of the helix formed by residues 67 - 79 (chain B) in PDB entry 3IEU
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 HIS 67 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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65B GLY* 4.2 17.8 + - - -
66B LEU* 1.3 81.5 + - - +
68B MET* 1.3 56.7 + - - +
69B GLU* 3.2 4.3 - - + +
70B GLU* 2.6 46.9 + - - +
71B LYS* 3.2 9.6 + - - -
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Residues in contact with MET 68 (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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4A ASP* 5.6 7.2 - - - +
5A LYS* 5.4 11.7 - - - -
66B LEU 4.4 0.2 + - - -
67B HIS* 1.3 72.0 - - - +
69B GLU* 1.3 62.9 + - - +
70B GLU 3.0 1.2 + - - -
71B LYS* 3.2 33.3 + - + +
72B ARG* 3.0 52.2 + - + +
82B ALA 6.0 1.1 - - - +
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Residues in contact with GLU 69 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44B ARG* 3.8 29.4 + - + +
67B HIS* 3.0 4.1 + - + +
68B MET* 1.3 77.1 - - - +
70B GLU* 1.3 65.6 + - + +
72B ARG* 3.5 19.3 + - - +
73B ALA* 3.1 22.5 + - - +
76B ARG* 4.6 0.9 + - - +
308B SO4 3.5 17.5 + - - +
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Residues in contact with GLU 70 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44B ARG 3.2 22.7 - - - +
45B HIS* 4.8 1.3 - - - -
46B ARG* 3.0 39.7 + - + -
63B THR* 4.7 2.6 + - - +
65B GLY 4.0 5.3 - - - +
66B LEU* 3.8 13.0 - - + -
67B HIS* 2.6 45.5 + - - +
69B GLU* 1.3 79.1 - - + +
71B LYS* 1.3 60.6 + - - +
72B ARG 3.0 1.3 - - - -
73B ALA* 2.9 3.1 + - - +
74B ILE* 2.8 34.9 + - - +
304B SO4 4.7 3.8 + - - -
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Residues in contact with LYS 71 (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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5A LYS* 4.4 11.7 - - - +
66B LEU* 3.6 28.6 + - + +
67B HIS 3.2 9.1 + - - +
68B MET* 3.9 31.9 - - + +
70B GLU* 1.3 77.6 - - - +
72B ARG* 1.3 62.3 + - - +
74B ILE* 4.2 4.0 - - - +
75B ASN* 3.0 24.1 + - - +
82B ALA 5.6 0.2 - - - -
86B ILE* 3.3 52.1 - - + +
87B GLY 2.8 23.6 + - - -
88B ASP* 3.1 21.7 + - - -
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Residues in contact with ARG 72 (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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68B MET* 3.0 52.8 + - + +
69B GLU* 3.6 15.5 - - - +
70B GLU 3.0 1.0 - - - -
71B LYS* 1.3 78.7 - - - +
73B ALA* 1.3 62.1 + - - +
75B ASN* 3.3 6.7 + - - +
76B ARG* 3.1 29.7 + - - +
82B ALA* 4.1 32.9 - - + +
308B SO4 2.7 58.5 + - - +
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Residues in contact with ALA 73 (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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44B ARG* 3.3 46.9 - - + +
45B HIS* 3.8 5.9 - - + +
69B GLU 3.1 11.7 + - - +
70B GLU 2.9 3.9 + - - +
72B ARG* 1.3 78.9 - - - +
74B ILE* 1.3 55.3 + - - +
76B ARG* 3.3 21.3 + - - +
77B LEU* 3.0 27.5 + - - +
310B SO4 4.6 7.3 + - - +
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Residues in contact with ILE 74 (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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10B PHE* 4.2 18.4 - - + -
45B HIS* 3.6 31.2 - - + +
47B ILE* 4.1 20.0 - - + -
66B LEU* 4.1 31.2 - - + -
70B GLU 2.8 22.2 + - - +
71B LYS* 3.6 8.1 - - - +
73B ALA* 1.3 74.1 - - - +
75B ASN* 1.3 65.6 + - - +
77B LEU* 3.4 7.7 - - - +
78B MET* 3.2 33.9 + - + +
86B ILE* 3.7 16.6 - - + -
180B PHE* 4.5 3.8 - - + -
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Residues in contact with ASN 75 (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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71B LYS* 3.0 13.4 + - - +
72B ARG 3.3 4.5 + - - +
74B ILE* 1.3 74.7 - - - +
76B ARG* 1.3 53.7 + - - +
78B MET* 3.1 22.9 + - - +
79B ASN 2.8 28.8 + - - -
80B LYS* 2.8 31.6 + - - +
81B ALA 3.5 12.1 + - - +
82B ALA* 3.2 24.6 + - - -
84B SER* 2.9 32.5 + - - +
85B SER 5.0 0.2 - - - +
86B ILE* 3.8 14.8 - - - +
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Residues in contact with ARG 76 (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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44B ARG* 5.2 7.9 - - - +
69B GLU* 4.6 1.0 + - - +
72B ARG* 3.1 18.6 + - - +
73B ALA* 3.5 33.4 - - - +
75B ASN* 1.3 74.5 - - - +
77B LEU* 1.3 56.8 + - - +
79B ASN* 2.8 34.8 + - - +
80B LYS 4.6 1.8 + - - -
82B ALA* 5.8 5.3 - - + +
188B ARG* 4.6 2.0 + - - -
308B SO4 3.2 34.4 + - - -
310B SO4 4.7 13.5 + - - +
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Residues in contact with LEU 77 (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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45B HIS* 4.0 28.7 - - + +
47B ILE* 3.9 27.4 - - + -
73B ALA 3.0 10.0 + - - +
74B ILE* 3.4 9.0 - - - +
76B ARG* 1.3 80.2 - - - +
78B MET* 1.3 51.7 + - - +
79B ASN* 4.0 3.1 - - - +
180B PHE* 4.1 13.0 - - + -
184B TYR* 2.6 38.0 + - + -
185B ILE 4.3 0.9 - - - +
186B THR* 4.1 31.6 - - - +
188B ARG* 4.0 31.6 + - - +
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Residues in contact with MET 78 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177A THR* 6.0 0.2 - - - +
181A PRO* 3.7 16.8 - - - +
74B ILE* 3.2 25.8 + - + +
75B ASN* 3.1 28.6 + - - +
76B ARG 3.1 0.4 - - - -
77B LEU* 1.3 76.1 - - - +
79B ASN* 1.3 71.9 + - - +
80B LYS* 3.9 23.2 - - + +
86B ILE* 4.7 4.0 - - + -
179B HIS* 3.8 47.3 - - + +
180B PHE* 3.4 33.4 - - + -
181B PRO* 5.9 0.4 - - - -
184B TYR* 3.6 11.9 + - + -
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Residues in contact with ASN 79 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
181A PRO* 3.2 9.4 - - + +
182A GLU* 2.8 27.9 + - - +
183A ASP 6.2 0.2 - - - +
75B ASN 2.8 1.0 + - - -
76B ARG* 2.8 24.2 + - - +
77B LEU 4.0 1.4 - - - +
78B MET* 1.3 82.1 - - - +
80B LYS* 1.3 61.0 + - - +
184B TYR* 3.8 10.2 + - - -
188B ARG* 4.2 14.9 + - - +
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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