Contacts of the helix formed by residues 59 - 71 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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55A PHE* 2.7 38.6 + + + +
58A LEU* 1.3 84.5 - - + +
60A GLN* 1.3 59.3 + - - +
61A PRO 3.4 0.4 - - - -
62A LEU* 3.7 15.0 + - + +
63A PHE* 3.0 32.3 + - + +
113A TYR* 3.8 35.9 - + - -
116A PHE* 3.5 54.7 - + + -
120A ALA* 5.0 0.4 - - + -
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Residues in contact with GLN 60 (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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55A PHE 3.7 3.1 + - - +
56A SER* 3.6 19.5 + - - +
59A PHE* 1.3 78.1 - - - +
61A PRO* 1.3 67.9 - - + +
63A PHE* 3.2 4.5 + - + +
64A GLY* 2.9 24.6 + - - -
119A ASN* 3.4 23.8 + - - -
120A ALA* 3.5 28.9 - - + +
123A PRO* 3.5 27.7 - - + +
355A CYS* 4.9 8.8 - - - -
359A GLN* 5.3 3.2 - - - +
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Residues in contact with PRO 61 (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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57A LEU 3.1 22.4 - - - +
58A LEU* 4.2 1.8 - - - +
59A PHE 3.7 3.1 - - - +
60A GLN* 1.3 90.5 - - + +
62A LEU* 1.3 67.4 + - - +
63A PHE 2.9 1.1 - - - -
64A GLY* 2.8 12.6 + - - -
65A LEU* 2.9 25.0 + - + +
351A LEU* 5.3 13.5 - - + -
355A CYS* 3.1 31.2 - - - -
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Residues in contact with LEU 62 (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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58A LEU 4.4 15.3 + - - +
59A PHE* 3.7 16.7 + - + +
60A GLN 3.5 0.2 - - - -
61A PRO* 1.3 79.1 - - - +
63A PHE* 1.3 63.3 + - + +
65A LEU* 3.3 13.1 + - - +
66A LEU* 3.0 70.3 + - + +
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Residues in contact with PHE 63 (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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59A PHE* 3.0 22.4 + + + +
60A GLN* 3.4 7.9 - - + +
61A PRO 2.9 0.8 - - - -
62A LEU* 1.3 80.9 - - + +
64A GLY* 1.3 59.6 + - - +
66A LEU* 3.7 12.3 + - + +
67A SER* 3.5 15.4 + - - -
76A LEU* 3.1 49.8 - - + +
80A ILE* 4.2 14.4 - - + -
116A PHE* 4.4 18.8 - + + -
120A ALA* 3.3 31.0 - - + -
121A GLY* 4.2 2.9 - - - -
123A PRO* 6.2 0.2 - - + -
124A ALA* 3.2 38.1 - - + -
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Residues in contact with GLY 64 (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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60A GLN 2.9 9.7 + - - -
61A PRO* 2.8 10.6 + - - -
63A PHE* 1.3 73.7 - - - +
65A LEU* 1.3 63.5 + - - +
66A LEU 3.2 1.8 - - - -
67A SER* 3.1 24.5 - - - -
68A ASP* 3.4 10.2 - - - +
205A HIS* 5.4 0.2 + - - -
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Residues in contact with LEU 65 (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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61A PRO* 2.9 25.0 + - + +
62A LEU* 3.8 12.6 - - - +
64A GLY* 1.3 77.1 - - - +
66A LEU* 1.3 63.7 + - + +
67A SER 3.1 0.4 - - - -
68A ASP* 3.2 24.2 + - - +
69A LYS* 3.7 9.2 + - - +
205A HIS* 6.0 2.9 - - + -
208A PHE* 3.9 35.0 - - + -
351A LEU* 5.3 3.8 - - + -
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Residues in contact with LEU 66 (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 LEU* 3.0 49.7 + - + +
63A PHE* 3.8 12.6 - - + +
65A LEU* 1.3 78.4 - - + +
67A SER* 1.3 55.9 + - - +
69A LYS* 3.6 19.9 + - + +
70A LEU* 2.7 42.9 + - + +
76A LEU* 4.7 18.8 - - + -
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Residues in contact with SER 67 (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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63A PHE 3.5 8.6 + - - -
64A GLY* 3.1 21.5 + - - -
65A LEU 3.1 0.4 - - - -
66A LEU* 1.3 79.7 - - - +
68A ASP* 1.3 58.5 + - - +
70A LEU* 3.7 12.4 - - - +
71A GLY* 2.9 30.8 + - - +
76A LEU* 5.4 1.8 - - - -
127A ALA* 5.1 11.2 - - - +
128A PHE* 5.6 3.1 + - - +
131A LYS* 3.9 13.6 + - - -
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Residues in contact with ASP 68 (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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64A GLY 3.4 12.4 - - - +
65A LEU* 3.2 21.1 - - - +
66A LEU 3.2 0.4 - - - -
67A SER* 1.3 77.0 - - - +
69A LYS* 1.3 57.9 + - - +
70A LEU 2.8 3.8 - - - -
71A GLY* 2.5 26.5 + - - +
131A LYS* 4.2 12.6 + - - +
199A ASN* 3.9 9.4 + - - -
205A HIS* 2.7 51.0 + - + +
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Residues in contact with LYS 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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65A LEU 3.7 8.2 + - - +
66A LEU* 3.6 20.5 + - + +
68A ASP* 1.3 77.6 - - - +
70A LEU* 1.3 60.2 + - + +
73A ARG* 4.1 17.3 + - - +
199A ASN* 4.9 4.0 + - - +
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Residues in contact with LEU 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 LEU* 2.7 33.7 + - + +
67A SER* 3.7 9.0 - - - +
68A ASP 2.8 0.2 - - - -
69A LYS* 1.3 80.4 - - + +
71A GLY* 1.3 66.9 + - - +
72A LEU 3.1 0.3 + - - -
73A ARG* 3.0 52.4 + - + +
75A TYR* 4.5 28.7 - - + -
76A LEU* 3.5 38.6 - - + -
199A ASN* 5.1 0.4 - - - -
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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
----------------------------------------------------------
67A SER* 2.9 16.7 + - - +
68A ASP* 2.5 23.1 + - - -
70A LEU* 1.3 75.9 - - - +
72A LEU* 1.3 58.0 + - - -
73A ARG 3.3 3.3 + - - +
128A PHE* 5.2 4.9 - - - -
131A LYS* 4.5 15.3 + - - +
199A ASN* 4.0 19.5 - - - -
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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
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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