Contacts of the helix formed by residues 75 - 83 (chain B) in PDB entry 7CAL
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 TRP 75 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71B ILE 3.5 11.9 + - - +
72B TYR* 3.0 11.5 + - + +
74B ALA* 1.3 77.9 - - - +
76B ILE* 1.3 74.8 + - + +
77B CYS 3.2 4.3 + - - -
78B PRO* 3.6 1.8 - - - +
79B PHE* 3.3 51.2 - + - +
210B HIS* 3.0 37.9 + + - -
247B TYR* 3.5 23.1 - + - -
701B 3PE 3.5 43.8 - - + +
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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
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72B TYR* 3.4 60.1 - - + +
73B SER* 4.4 1.3 - - - -
75B TRP* 1.3 94.6 - - + +
77B CYS* 1.3 64.8 - - - +
78B PRO 3.5 0.4 - - - -
79B PHE* 3.7 13.5 - - + -
80B GLN* 3.3 41.2 + - + +
91B ILE* 5.2 8.5 - - + -
95B ASP* 4.7 9.2 - - + -
171B ARG* 3.6 24.2 - - - +
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Residues in contact with CYS 77 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73B SER 3.3 18.8 + - - +
75B TRP 3.2 1.8 - - - +
76B ILE* 1.3 83.9 - - - +
78B PRO* 1.4 65.2 - - + +
80B GLN* 4.8 1.9 - - - +
81B PHE* 3.5 10.4 + - - +
168B SER* 3.3 27.8 + - - +
169B MET* 3.3 26.5 - - - +
171B ARG* 3.6 38.7 + - - +
172B LEU* 4.0 11.7 - - + -
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Residues in contact with PRO 78 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74B ALA 3.8 11.4 - - - +
75B TRP 3.6 7.0 - - - +
77B CYS* 1.4 92.0 - - + +
79B PHE* 1.3 61.1 + - - +
80B GLN 3.6 0.7 - - - -
81B PHE* 3.6 5.6 - - + +
82B ALA* 3.6 12.5 + - - +
169B MET* 3.7 10.8 - - + -
172B LEU* 4.9 6.3 - - + -
207B PHE* 5.0 1.3 - - + -
210B HIS* 3.5 25.8 - - + -
211B CYS* 4.4 15.9 - - + -
214B CYS* 3.4 22.5 - - + +
215B PHE* 4.0 24.2 - - + -
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Residues in contact with PHE 79 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75B TRP* 3.3 48.4 + + + +
76B ILE* 3.7 9.4 + - + -
77B CYS 3.5 1.0 - - - -
78B PRO* 1.3 79.3 - - - +
80B GLN* 1.3 65.6 + - + +
81B PHE 3.2 0.2 - - - -
82B ALA 3.5 0.2 + - - -
83B PHE* 3.0 63.1 + + + +
84B ILE* 3.7 12.8 + - + -
210B HIS* 4.1 5.4 - + - +
214B CYS* 4.4 4.5 - - - -
244B TRP 5.4 5.4 - - - -
245B ASN* 5.1 11.4 - - - -
247B TYR* 4.2 30.5 - + + -
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Residues in contact with GLN 80 (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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76B ILE* 3.3 27.5 + - + +
77B CYS* 4.8 2.9 + - - +
79B PHE* 1.3 80.2 - - + +
81B PHE* 1.3 64.3 + - - +
82B ALA 3.2 1.3 + - - -
84B ILE* 2.9 37.5 - - + +
87B LYS* 4.9 11.0 - - + +
91B ILE* 4.0 22.3 - - + +
95B ASP* 5.3 6.6 - - - +
165B ARG* 3.3 14.0 + - - +
168B SER* 4.4 5.1 + - - -
171B ARG* 3.4 31.9 - - - +
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Residues in contact with PHE 81 (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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77B CYS 3.5 18.1 + - - +
78B PRO 3.6 8.2 - - - +
79B PHE 3.2 0.6 - - - -
80B GLN* 1.3 82.8 - - - +
82B ALA* 1.3 59.8 + - + +
162B LEU* 5.5 3.1 - - + -
165B ARG* 3.4 64.9 + - + +
166B ILE* 4.0 26.5 - - + -
169B MET* 3.6 17.9 - - + -
214B CYS 5.0 0.2 - - - -
215B PHE* 3.8 26.0 - + - -
218B LEU* 3.5 41.4 - - + +
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Residues in contact with ALA 82 (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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78B PRO 3.6 8.9 + - - +
79B PHE 3.5 1.6 + - - -
80B GLN 4.7 0.4 - - - -
81B PHE* 1.3 81.7 - - + +
83B PHE* 1.3 77.9 + - + +
84B ILE 3.8 0.2 - - - -
85B THR* 4.1 12.4 - - - -
214B CYS 3.3 27.1 - - - +
217B TYR* 4.6 6.9 - - + -
218B LEU* 4.0 21.7 - - + +
221B ASP* 4.5 12.1 - - - +
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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
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79B PHE* 3.0 39.5 + + + +
82B ALA* 1.3 80.5 - - + +
84B ILE* 1.3 62.2 + - - +
85B THR* 3.0 8.7 + - - -
213B GLY 4.3 0.4 - - - -
214B CYS* 3.6 31.6 - - + -
217B TYR* 3.6 52.0 - + + -
221B ASP* 5.6 0.7 - - - +
244B TRP* 4.8 30.4 - + + +
247B TYR* 3.5 39.9 - + + -
250B ALA* 4.1 9.0 - - + -
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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