Contacts of the helix formed by residues 76 - 83 (chain B) in PDB entry 4XZC
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 PRO 76 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33B SER* 4.3 3.8 - - - -
34B ALA 4.6 0.4 - - - +
75B ALA* 1.4 84.9 - - + +
77B ILE* 1.3 60.8 + - - +
78B TYR 3.7 1.6 - - - -
79B GLU* 3.4 18.6 - - + +
80B CYS* 2.9 33.7 + - - +
413B SER* 4.5 7.6 - - - +
416B ASN* 3.3 31.2 - - + +
465B CYS* 3.7 26.7 - - - -
466B HIS* 4.2 16.8 - - + +
467B PHE* 4.3 7.0 - - + -
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Residues in contact with ILE 77 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13B TYR* 4.1 0.7 + - - -
17B PHE* 4.6 4.0 - - + -
20B TYR* 4.2 26.7 - - + +
26B LEU* 3.8 31.6 - - + -
34B ALA 3.7 13.9 + - - +
35B SER* 4.2 2.9 - - - -
36B PHE* 4.0 25.6 - - + -
75B ALA* 3.3 16.1 + - + +
76B PRO* 1.3 68.9 - - - +
78B TYR* 1.3 69.7 + - - +
79B GLU* 3.1 1.9 + - - -
80B CYS* 3.1 2.1 + - - +
81B GLY* 3.0 22.2 + - - -
395B VAL* 3.7 28.0 - - + -
396B VAL* 4.2 12.9 - - + +
404B ALA* 5.0 0.9 - - + -
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Residues in contact with TYR 78 (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 LYS* 3.4 15.9 + - - +
13B TYR* 2.8 34.0 + + - -
14B ASP* 2.7 27.2 + - - -
17B PHE* 3.3 59.3 - + + -
26B LEU* 5.5 0.4 - - - +
33B SER* 3.9 11.7 + - - +
34B ALA 4.7 1.0 + - - -
77B ILE* 1.3 78.5 - - - +
79B GLU* 1.3 83.4 + - + +
82B TRP* 3.3 5.2 + - - +
141B ILE* 4.0 25.7 - - + +
142B ASN* 4.4 11.4 - - + -
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Residues in contact with GLU 79 (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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33B SER* 3.0 34.5 + - - -
76B PRO* 3.4 12.9 - - + +
77B ILE 3.1 0.2 - - - -
78B TYR* 1.3 82.1 + - + +
80B CYS* 1.3 67.2 + - - +
82B TRP* 3.3 7.8 + - - +
83B ALA* 3.1 23.6 + - - +
139B PHE* 5.7 0.2 - - - -
142B ASN* 2.8 27.0 + - - +
144B TYR* 3.6 25.6 - - + -
145B THR* 4.1 18.1 - - + +
465B CYS* 4.3 3.4 - - - -
467B PHE* 3.3 23.7 - - + -
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Residues in contact with CYS 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 PRO* 2.9 28.9 + - - +
77B ILE 3.1 4.0 + - - +
79B GLU* 1.3 77.8 - - - +
81B GLY* 1.3 61.8 + - - +
83B ALA* 3.6 2.1 + - - +
84B CYS* 3.3 29.2 + - - +
391B ALA 3.4 24.9 - - - -
392B CYS 4.1 5.3 - - - +
395B VAL* 3.5 35.4 - - + -
396B VAL* 4.1 7.6 - - + +
467B PHE* 3.6 19.5 - - - -
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Residues in contact with GLY 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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5B ILE* 4.3 13.3 - - - +
13B TYR* 3.2 21.6 - - - -
16B TRP* 5.3 2.7 - - - -
77B ILE 3.0 12.8 + - - -
80B CYS* 1.3 74.6 - - - +
82B TRP* 1.3 65.6 + - - +
84B CYS* 2.9 8.2 + - - +
85B CYS* 2.9 21.1 + - - -
396B VAL* 4.3 8.4 - - - +
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Residues in contact with TRP 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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8B ASN 4.8 6.5 - - - -
9B THR* 4.1 4.0 - - - -
10B LYS* 3.5 42.0 - - + -
13B TYR* 3.0 41.7 + + + -
78B TYR 3.3 8.7 + - - +
79B GLU* 3.3 11.1 + - - +
81B GLY* 1.3 73.5 - - - +
83B ALA* 1.3 56.7 + - - +
84B CYS 2.7 10.9 + - - -
85B CYS* 3.1 30.5 + - - -
88B MET* 3.4 35.7 - - + +
137B ASN 4.9 0.9 - - - -
138B LYS* 3.6 19.1 - - + -
139B PHE* 3.0 37.8 + + - -
141B ILE* 3.4 31.9 - - + -
145B THR* 4.8 4.9 - - + -
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Residues in contact with ALA 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 GLU 3.1 9.1 + - - +
80B CYS 3.9 3.8 - - - +
81B GLY 3.4 0.2 - - - -
82B TRP* 1.3 76.9 - - - +
84B CYS* 1.3 53.1 + - - +
88B MET* 4.0 10.3 - - - -
139B PHE* 4.0 11.9 - - + -
308B ILE* 3.8 14.6 - - + -
312B TYR* 2.4 34.2 + - - -
392B CYS 4.8 3.8 - - - +
393B PHE* 4.0 4.3 - - - -
467B PHE* 3.7 32.8 - - + -
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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