Contacts of the helix formed by residues 68 - 75 (chain A) in PDB entry 5V6Y
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 ARG 68 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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46A GLU* 3.9 33.0 + - + +
47A GLU* 5.4 9.6 + - - +
64A TRP* 3.5 33.6 - - + +
65A ALA 3.5 0.9 + - - +
66A HIS 3.2 0.8 - - - -
67A ASP* 1.3 88.4 + - - +
69A PHE* 1.3 64.1 + - + +
70A GLY 3.3 1.7 + - - -
71A GLY* 3.5 4.6 + - - +
72A TYR* 3.3 45.1 + - + +
338A MET* 5.9 0.9 - - - -
339A SER* 3.3 38.0 + - - +
342A TRP* 4.0 24.8 - - - +
343A TYR* 5.3 1.0 - - - +
346A ARG* 4.4 15.2 - - - +
2115A PRO* 5.6 4.2 - - - +
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Residues in contact with PHE 69 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62A ILE* 3.8 18.4 - - + -
64A TRP* 3.1 34.3 - - + -
65A ALA 3.2 19.3 - - - -
66A HIS* 3.3 17.1 + - + +
68A ARG* 1.3 77.4 - - - +
70A GLY* 1.3 60.5 + - - +
72A TYR* 3.3 12.0 + + - +
73A ALA* 2.8 30.0 + - - +
78A LEU* 3.5 21.2 - - + +
99A VAL* 6.2 2.5 - - + -
106A ILE* 3.4 15.6 - - + +
107A ALA* 3.7 15.0 - - + -
265A SER* 3.4 28.0 - - - -
267A GLY* 3.4 26.2 - - - -
334A ASN* 5.9 0.2 - - + -
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Residues in contact with GLY 70 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66A HIS 4.3 2.8 + - - -
68A ARG 3.3 0.8 - - - -
69A PHE* 1.3 77.2 - - - +
71A GLY* 1.3 60.8 + - - +
73A ALA* 3.3 1.7 + - - +
74A GLN* 2.8 31.2 + - - +
101A TYR* 4.1 22.4 - - - -
106A ILE* 4.3 2.1 - - - +
334A ASN* 3.0 27.0 + - - +
336A PRO* 4.3 4.9 - - - -
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Residues in contact with GLY 71 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67A ASP 5.1 0.8 + - - -
68A ARG* 3.5 7.0 + - - +
69A PHE 3.4 0.4 - - - -
70A GLY* 1.3 75.5 - - - +
72A TYR* 1.3 64.4 + - - +
74A GLN* 4.0 2.7 - - - +
75A SER* 3.2 25.8 + - - -
77A LEU* 5.3 0.2 - - - +
334A ASN 4.2 0.6 + - - -
335A ILE 4.8 0.4 + - - -
336A PRO* 4.0 28.3 - - - +
339A SER* 5.7 2.0 - - - -
2115A PRO* 5.8 8.8 - - - +
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Residues in contact with TYR 72 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45A LEU 4.3 1.6 + - - -
46A GLU* 2.8 36.9 + - - +
49A PHE* 3.7 30.3 - + + -
50A PRO* 3.7 32.3 - - + +
62A ILE* 3.9 14.2 - - + +
64A TRP* 5.4 2.4 - - + -
68A ARG* 3.3 33.6 + - + +
69A PHE* 3.3 28.4 + + - +
70A GLY 3.2 0.4 - - - -
71A GLY* 1.3 78.4 - - - +
73A ALA* 1.3 62.3 + - - +
75A SER* 3.2 8.0 + - - -
77A LEU* 3.0 30.7 + - + +
78A LEU* 3.6 18.4 - - + -
2115A PRO* 6.4 0.4 - - + -
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Residues in contact with ALA 73 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69A PHE 2.8 20.5 + - - +
70A GLY 3.3 3.1 + - - +
72A TYR* 1.3 73.3 - - - +
74A GLN* 1.3 63.3 + - - +
76A GLY* 3.1 13.0 + - - +
78A LEU* 3.9 15.4 - - + +
101A TYR* 3.9 17.5 - - + -
106A ILE* 3.7 29.8 - - + -
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Residues in contact with GLN 74 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70A GLY 2.8 16.6 + - - +
71A GLY* 4.0 4.6 - - - +
72A TYR 3.3 0.4 - - - -
73A ALA* 1.3 77.0 - - - +
75A SER* 1.3 60.8 + - - +
76A GLY 3.1 1.4 + - - -
101A TYR* 3.8 21.8 + - + +
336A PRO* 3.3 31.6 - - + +
337A GLN* 5.8 2.2 - - - +
2118A ASN* 5.1 9.5 + - - +
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Residues in contact with SER 75 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50A PRO* 6.1 0.3 - - - +
71A GLY 3.2 15.8 + - - -
72A TYR 3.2 6.2 + - - -
74A GLN* 1.3 78.1 + - - +
76A GLY* 1.3 60.7 + - - +
77A LEU* 3.5 26.3 + - - +
2115A PRO* 5.9 2.6 - - - +
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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