Contacts of the helix formed by residues 59 - 70 (chain B) in PDB entry 1PV7
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 PHE 59 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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55B PHE* 2.7 38.7 + + + +
58B LEU* 1.3 84.3 - - + +
60B GLN* 1.3 59.0 + - - +
61B PRO 3.4 0.9 - - - -
62B LEU* 3.7 14.2 + - + +
63B PHE* 3.0 31.6 + + + +
113B TYR* 3.9 34.3 - + - -
116B PHE* 3.5 55.9 - + + -
120B ALA* 5.1 0.7 - - + -
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Residues in contact with GLN 60 (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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55B PHE 3.8 3.1 + - - +
56B SER* 3.6 18.9 + - - +
59B PHE* 1.3 78.0 - - - +
61B PRO* 1.3 69.3 - - + +
63B PHE* 3.2 4.9 + - + +
64B GLY* 2.8 24.3 + - - -
119B ASN* 3.4 25.5 + - - -
120B ALA* 3.6 25.7 - - + +
123B PRO* 3.5 26.8 - - + +
355B CYS* 4.8 9.8 - - - -
359B GLN* 5.5 2.8 - - - +
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Residues in contact with PRO 61 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57B LEU 3.2 23.1 - - - +
58B LEU 4.3 0.9 - - - +
59B PHE 3.7 3.1 - - - +
60B GLN* 1.3 90.7 - - + +
62B LEU* 1.3 68.7 + - - +
63B PHE 2.9 0.9 - - - -
64B GLY* 2.8 13.1 + - - -
65B LEU* 2.9 25.8 + - + +
351B LEU* 5.2 13.7 - - + -
355B CYS* 3.1 30.3 - - + -
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Residues in contact with LEU 62 (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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58B LEU 4.4 15.4 + - - +
59B PHE* 3.7 16.9 + - + +
61B PRO* 1.3 80.2 - - - +
63B PHE* 1.3 65.4 + - + +
65B LEU* 3.2 14.6 + - + +
66B LEU* 3.0 69.7 + - + +
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Residues in contact with PHE 63 (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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59B PHE* 3.0 23.5 + + + +
60B GLN* 3.4 9.0 - - + +
61B PRO 2.9 0.6 - - - -
62B LEU* 1.3 79.7 - - + +
64B GLY* 1.3 59.8 + - - +
66B LEU* 3.8 11.6 + - + +
67B SER* 3.5 15.2 + - - -
76B LEU* 3.4 45.7 - - + +
80B ILE* 4.1 15.3 - - + -
116B PHE* 4.3 20.2 - + + -
120B ALA* 3.4 31.0 - - + -
121B GLY* 4.2 4.0 - - - -
124B ALA* 3.2 39.0 - - + -
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Residues in contact with GLY 64 (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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60B GLN 2.8 16.3 + - - -
61B PRO* 2.8 3.8 + - - -
63B PHE* 1.3 73.5 - - - +
65B LEU* 1.3 63.8 + - - +
66B LEU 3.2 1.3 - - - -
67B SER* 3.1 25.2 - - - -
68B ASP* 3.2 10.6 - - - +
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Residues in contact with LEU 65 (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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61B PRO* 2.9 30.2 + - + +
62B LEU* 3.6 13.5 - - + +
64B GLY* 1.3 76.2 - - - +
66B LEU* 1.3 63.2 + - + +
68B ASP* 3.1 26.5 + - - +
69B LYS* 3.7 6.4 + - - +
205B HIS* 6.1 2.9 - - + -
208B PHE* 3.9 35.0 - - + -
351B LEU* 5.3 4.5 - - + -
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Residues in contact with LEU 66 (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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62B LEU* 3.0 49.9 + - + +
63B PHE* 3.9 11.4 - - + +
65B LEU* 1.3 77.0 - - + +
67B SER* 1.3 56.9 + - - +
68B ASP 3.1 0.2 - - - -
69B LYS* 3.6 19.4 + - + +
70B LEU* 2.7 42.2 + - + +
76B LEU* 4.6 18.8 - - + -
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Residues in contact with SER 67 (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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63B PHE 3.5 7.6 + - - -
64B GLY* 3.1 22.3 + - - -
65B LEU 3.1 0.8 - - - -
66B LEU* 1.3 79.4 - - - +
68B ASP* 1.3 56.3 + - - +
70B LEU* 3.8 12.1 - - - +
71B GLY* 3.1 29.3 + - - +
76B LEU* 5.3 1.3 - - - -
127B ALA* 5.1 11.0 - - - +
128B PHE* 5.6 3.1 + - - +
131B LYS* 3.7 15.0 + - - -
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Residues in contact with ASP 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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64B GLY 3.2 12.9 - - - +
65B LEU* 3.1 22.3 - - - +
66B LEU 3.1 0.4 - - - -
67B SER* 1.3 76.4 - - - +
69B LYS* 1.3 58.2 + - - +
70B LEU 2.9 3.8 - - - -
71B GLY* 2.5 25.5 + - - -
131B LYS* 4.2 13.4 + - - +
199B ASN* 3.8 9.2 + - - -
205B HIS* 2.6 51.3 + - + +
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Residues in contact with LYS 69 (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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65B LEU 3.7 7.6 + - - +
66B LEU* 3.6 21.6 + - + +
68B ASP* 1.3 79.4 - - - +
70B LEU* 1.3 60.9 + - + +
73B ARG* 4.1 16.7 + - - +
199B ASN* 4.9 3.9 + - - +
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Residues in contact with LEU 70 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66B LEU* 2.7 30.6 + - + +
67B SER* 3.8 11.4 - - - +
68B ASP 2.9 0.6 - - - -
69B LYS* 1.3 80.0 - - + +
71B GLY* 1.3 66.3 + - - +
72B LEU 3.2 0.2 + - - -
73B ARG* 3.0 53.5 + - + +
75B TYR* 4.5 25.8 - - + -
76B LEU* 3.5 41.1 - - + -
199B ASN* 5.0 0.4 - - - -
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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