Contacts of the helix formed by residues 75 - 90 (chain B) in PDB entry 1EWV
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 GLY 75 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51B PHE* 4.5 1.0 - - - +
52B SER 2.7 25.0 + - - -
53B VAL* 3.9 2.0 - - - -
71B ARG* 2.8 14.3 + - - +
73B GLN 3.3 3.2 - - - -
74B TYR* 1.4 76.5 - - - +
76B ILE* 1.4 67.0 + - - +
77B GLN 3.4 1.3 - - - -
78B ARG* 3.2 12.7 + - - +
79B VAL* 3.2 21.6 + - - +
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Residues in contact with ILE 76 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53B VAL* 3.5 26.7 - - + -
70B ILE* 3.9 13.9 - - + -
71B ARG 2.6 16.8 + - - +
72B GLU* 3.6 10.0 - - - +
75B GLY* 1.4 67.2 - - - +
77B GLN* 1.3 64.8 + - - +
78B ARG 2.9 7.1 + - - -
79B VAL* 3.2 2.5 + - + +
80B GLU* 3.0 22.5 + - + +
354B PHE* 4.3 7.9 - - + -
365B ASN* 4.5 11.0 - - - +
367B TRP* 3.9 13.0 - - + -
368B PHE* 4.0 15.0 - - + +
371B PHE* 3.5 51.6 - - + -
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Residues in contact with GLN 77 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72B GLU* 3.2 45.4 + - + +
73B GLN* 4.3 7.8 - - - +
76B ILE* 1.3 79.4 - - - +
78B ARG* 1.3 59.1 + - - +
80B GLU 4.0 0.4 - - - -
81B ALA* 2.9 22.6 + - - +
350B PHE* 3.1 24.9 - - + -
354B PHE* 3.7 25.1 - - + -
404B TYR* 3.4 21.7 + - - -
405B VAL 3.5 8.5 + - - -
406B GLN* 3.4 3.5 - - - -
407B ASP* 2.6 33.7 + - + +
410B MET* 3.9 8.3 - - + +
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Residues in contact with ARG 78 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51B PHE* 3.5 30.0 - - + -
52B SER* 5.0 3.6 - - - +
73B GLN 4.7 0.7 - - - +
74B TYR* 3.0 50.9 + - - +
75B GLY 3.2 5.6 + - - +
76B ILE 2.9 0.6 - - - -
77B GLN* 1.3 77.3 - - - +
79B VAL* 1.3 55.6 + - - +
80B GLU 3.1 1.6 - - - -
81B ALA* 2.5 11.4 + - + +
82B MET* 2.4 38.4 + - - +
110B TRP* 4.8 8.1 - - - -
163B GLY* 5.3 4.4 - - - -
185B TYR* 3.6 28.1 + - - -
186B SER* 5.3 3.6 - - - -
407B ASP* 2.9 28.8 + - + +
409B LYS* 3.7 25.9 - - - +
410B MET* 5.4 2.7 - - + -
413B VAL* 3.5 17.7 - - + +
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Residues in contact with VAL 79 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39B ALA* 4.0 15.5 - - + -
51B PHE* 4.3 13.0 - - + -
53B VAL* 4.2 24.2 - - + -
75B GLY 3.2 20.6 - - - +
76B ILE* 3.2 5.8 + - - +
78B ARG* 1.3 75.5 - - - +
80B GLU* 1.4 58.7 + - - +
82B MET* 3.3 7.4 + - - +
83B PHE* 3.1 31.1 + - + -
105B ILE* 3.8 23.3 - - + +
365B ASN* 3.2 25.8 - - - +
367B TRP* 4.1 4.7 - - + -
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Residues in contact with GLU 80 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76B ILE* 3.0 18.4 + - + +
77B GLN 4.0 3.6 - - - +
79B VAL* 1.4 77.7 - - - +
81B ALA* 1.3 57.0 + - - +
83B PHE* 4.0 7.2 - - - -
84B HIS* 3.1 26.7 + - - +
350B PHE* 4.4 1.1 - - + -
353B TYR* 2.7 42.8 + - + -
354B PHE* 4.4 10.1 - - + -
357B LEU* 4.1 5.3 - - + +
362B ASN* 3.0 35.5 + - - +
364B ARG* 4.4 2.9 + - - -
365B ASN* 3.0 17.8 - - - +
368B PHE* 3.2 30.3 - - + -
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Residues in contact with ALA 81 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77B GLN 2.9 20.2 + - - +
78B ARG* 2.5 20.0 + - - +
80B GLU* 1.3 73.2 - - - +
82B MET* 1.3 57.9 + - - +
83B PHE 3.2 0.4 - - - -
84B HIS* 3.8 3.8 - - - -
85B THR* 3.0 35.3 + - - +
350B PHE* 3.6 16.2 - - + -
410B MET* 3.7 15.5 - - - -
413B VAL* 4.9 7.9 - - + -
414B ILE* 5.1 4.3 - - + -
417B ILE* 4.0 2.0 - - - +
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Residues in contact with MET 82 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47B ILE* 3.5 24.5 - - + +
49B ALA* 3.3 30.5 - - + -
51B PHE* 3.6 19.5 - - + -
78B ARG 2.4 27.3 + - - +
79B VAL 3.7 0.7 - - - +
81B ALA* 1.3 71.3 - - - +
83B PHE* 1.3 59.4 + - - +
86B LEU* 3.3 34.3 + - + +
103B SER* 4.1 14.1 - - - -
105B ILE* 3.1 30.1 - - + -
160B ILE* 4.5 9.2 - - + -
413B VAL* 5.7 0.2 - - - -
417B ILE* 3.4 32.4 - - + +
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Residues in contact with PHE 83 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39B ALA* 3.5 39.9 - - + -
40B ARG 3.9 7.0 - - - -
41B MET* 4.1 20.4 - - + +
79B VAL* 3.1 20.4 + - + +
80B GLU* 4.0 10.3 - - - +
82B MET* 1.3 75.2 - - - +
84B HIS* 1.3 61.4 + - - +
86B LEU* 3.6 4.5 + - - +
87B ASP* 2.6 33.0 + - - +
103B SER* 3.2 26.5 - - - -
105B ILE* 3.6 8.1 - - + -
364B ARG* 3.6 51.1 + - + +
365B ASN* 3.9 17.5 - - + -
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Residues in contact with HIS 84 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80B GLU 3.1 18.0 + - - +
81B ALA* 4.0 4.9 - - - +
83B PHE* 1.3 78.0 - - - +
85B THR* 1.3 71.1 + - - +
87B ASP* 2.8 35.7 - - + +
88B LYS* 3.0 16.6 + - + +
349B SER* 4.3 17.3 + - - -
350B PHE* 4.4 19.4 + + + -
353B TYR* 3.7 47.9 - + + +
364B ARG* 4.7 0.2 - - - +
414B ILE* 6.4 1.8 - - + -
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Residues in contact with THR 85 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81B ALA 3.0 18.4 + - - -
84B HIS* 1.3 87.1 - - - +
86B LEU* 1.3 63.2 + - - +
88B LYS* 2.9 14.8 + - - +
89B ILE* 2.8 25.3 + - + +
414B ILE* 3.5 24.2 - - + +
417B ILE* 3.2 41.2 - - + +
418B TYR* 3.6 18.8 - - + -
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Residues in contact with LEU 86 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41B MET* 4.4 12.6 - - - -
47B ILE* 4.6 6.7 - - + +
82B MET* 3.3 31.8 + - + +
83B PHE* 3.9 4.9 - - - +
84B HIS 3.3 0.2 - - - -
85B THR* 1.3 79.7 - - - +
87B ASP* 1.3 61.1 + - - +
89B ILE* 3.4 20.4 + - + +
90B ASN* 2.9 32.1 + - - -
101B LEU* 3.6 35.9 - - + +
102B GLY 4.1 13.0 - - - +
103B SER* 3.6 31.4 - - - +
417B ILE* 4.4 9.2 - - + -
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Residues in contact with ASP 87 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41B MET* 3.7 17.3 - - - +
83B PHE 2.6 26.2 + - - +
84B HIS* 2.8 19.5 + - + +
86B LEU* 1.3 78.4 - - - +
88B LYS* 1.3 58.3 + - - +
89B ILE 3.0 0.2 - - - -
90B ASN* 3.2 8.3 + - - +
91B ALA* 3.0 23.4 + - - +
353B TYR* 5.4 1.2 - - - -
364B ARG* 3.2 25.5 + - - -
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Residues in contact with LYS 88 (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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84B HIS* 3.0 18.3 + - + +
85B THR* 2.9 10.8 + - - +
87B ASP* 1.3 79.1 - - - +
89B ILE* 1.3 58.4 + - - +
91B ALA* 3.5 13.0 - - + +
92B ASP* 3.2 29.2 + - - +
418B TYR* 4.0 19.3 + - - +
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Residues in contact with ILE 89 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85B THR* 2.8 39.0 - - + +
86B LEU* 3.6 26.9 - - + +
87B ASP 3.0 0.2 - - - -
88B LYS* 1.3 77.6 - - - +
90B ASN* 1.3 62.3 + - - +
91B ALA 2.9 7.4 + - - -
92B ASP* 3.2 23.6 + - - +
95B LEU* 3.4 38.5 - - + +
96B LEU* 4.4 11.6 - - + +
101B LEU* 5.2 2.9 - - + -
417B ILE* 3.8 8.3 - - + -
418B TYR* 4.4 19.3 - - + -
421B ALA* 4.8 13.5 - - + -
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Residues in contact with ASN 90 (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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41B MET* 5.1 5.5 - - - +
86B LEU* 2.9 24.0 + - - +
87B ASP* 3.2 7.2 + - - +
89B ILE* 1.3 78.9 - - - +
91B ALA* 1.3 57.9 + - - +
92B ASP 3.5 2.2 - - - +
96B LEU* 5.0 5.7 - - - +
99B ILE 3.9 4.9 - - - +
100B THR* 3.3 34.8 - - + +
101B LEU* 3.4 28.5 + - - +
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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
------------------------------------------------------------
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