Contacts of the helix formed by residues 67 - 81 (chain A) in PDB entry 1PVQ
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 GLU 67 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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62A LYS 4.8 1.8 + - - -
65A PRO 3.6 3.9 + - - +
66A ALA* 1.3 72.3 - - - +
68A PRO* 1.3 85.4 - - + +
69A GLU* 3.2 41.0 + - - +
70A ASP* 2.9 41.4 + - - +
71A VAL* 3.0 14.3 + - - +
107A PRO* 6.1 0.2 - - - -
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Residues in contact with PRO 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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66A ALA 3.7 7.9 - - - +
67A GLU* 1.3 98.9 - - + +
69A GLU* 1.3 65.1 + - - +
71A VAL* 3.2 4.7 + - + +
72A ARG* 2.9 23.7 + - - +
107A PRO* 5.5 5.8 - - + -
110A SER* 3.6 33.2 - - - +
112A ALA* 4.8 8.5 - - + -
113A VAL* 3.8 9.6 - - + +
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Residues in contact with GLU 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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67A GLU* 3.2 23.7 + - - +
68A PRO* 1.3 79.0 - - + +
70A ASP* 1.3 60.6 + - - +
72A ARG* 3.2 17.9 + - - +
73A ASP* 2.9 37.0 + - - +
112A ALA* 3.6 25.3 - - - +
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Residues in contact with ASP 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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52A TRP* 3.8 18.4 - - + -
55A TRP* 3.7 7.8 - - + -
61A ARG* 3.3 43.1 + - + +
62A LYS* 4.5 6.2 + - - +
67A GLU* 2.9 36.0 + - + +
69A GLU* 1.3 78.1 - - - +
71A VAL* 1.3 60.7 + - - +
73A ASP* 3.0 10.0 + - - +
74A TYR* 2.9 27.4 + - - +
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Residues in contact with VAL 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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52A TRP* 3.9 16.2 - - + -
66A ALA* 3.8 24.9 - - + -
67A GLU 3.0 18.2 + - - +
68A PRO 3.8 4.7 - - - +
70A ASP* 1.3 74.6 - - - +
72A ARG* 1.3 62.5 + - - +
74A TYR* 3.3 2.2 + - + +
75A LEU* 3.0 43.9 + - + +
92A LEU* 4.6 3.8 - - + -
95A LEU* 4.2 19.3 - - + -
107A PRO* 3.9 25.1 - - + -
113A VAL* 4.2 8.7 - - + -
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Residues in contact with ARG 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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68A PRO 2.9 13.5 + - - +
69A GLU* 3.3 23.6 + - - +
71A VAL* 1.3 78.2 - - - +
73A ASP* 1.3 72.9 + - - +
75A LEU* 3.3 3.6 + - - +
76A LEU* 3.2 44.6 + - - +
112A ALA* 3.8 31.8 + - + +
113A VAL* 4.5 2.9 - - + +
116A VAL* 4.1 31.0 - - + +
119A ARG* 3.9 22.2 - - - +
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Residues in contact with ASP 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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55A TRP* 3.4 20.1 - - + -
61A ARG* 2.6 30.4 + - - +
69A GLU* 2.9 21.2 + - - +
70A ASP 3.3 8.5 - - - +
72A ARG* 1.3 90.6 + - - +
74A TYR* 1.3 56.6 + - - +
76A LEU* 3.6 8.6 + - - +
77A TYR* 3.1 24.9 + - - +
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Residues in contact with TYR 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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48A VAL* 4.0 1.8 + - + -
51A SER* 2.3 46.1 + - - -
52A TRP* 3.7 38.1 + + + -
55A TRP* 3.7 30.2 - + + -
70A ASP 2.9 11.8 + - - +
71A VAL 3.6 7.2 - - - +
72A ARG 3.2 0.2 - - - -
73A ASP* 1.3 76.7 - - - +
75A LEU* 1.3 68.1 + - + +
76A LEU 3.2 0.2 - - - -
77A TYR* 3.2 13.4 - + - +
78A LEU* 2.9 52.8 + - + +
91A HIS* 2.5 38.0 + - + -
95A LEU* 4.8 9.2 - - + -
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Residues in contact with LEU 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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71A VAL* 3.0 35.5 + - + +
72A ARG* 3.3 4.0 + - - +
74A TYR* 1.3 82.4 - - + +
76A LEU* 1.3 61.6 + - - +
78A LEU* 3.3 13.9 + - + +
79A GLN* 3.0 22.2 + - - +
88A ILE* 3.5 38.3 - - + +
91A HIS* 4.6 0.4 - - + -
92A LEU* 3.9 27.6 - - + +
95A LEU* 5.9 0.2 - - + -
113A VAL* 4.4 5.2 - - + -
116A VAL* 4.3 15.9 - - + -
117A MET* 3.8 20.2 - - - -
120A ILE* 3.6 18.4 - - + +
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Residues in contact with LEU 76 (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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72A ARG* 3.2 50.3 + - - +
73A ASP* 3.8 6.5 - - - +
74A TYR 3.2 0.2 - - - -
75A LEU* 1.3 74.0 - - - +
77A TYR* 1.3 60.9 + - - +
79A GLN* 3.2 15.0 + - - +
80A ALA* 2.8 32.2 + - - +
116A VAL* 3.2 25.6 - - + -
119A ARG* 4.2 20.6 - - - +
120A ILE* 3.7 15.3 - - + -
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Residues in contact with TYR 77 (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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51A SER* 5.4 2.2 - - - -
55A TRP* 3.5 39.7 - + + +
58A LEU* 5.6 6.9 - - + +
73A ASP 3.1 16.5 + - - +
74A TYR* 3.2 19.5 - + - +
76A LEU* 1.3 77.2 - - - +
78A LEU* 1.3 72.0 + - + +
80A ALA* 3.5 7.2 + - + +
81A ARG* 2.9 61.2 + - + +
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Residues in contact with LEU 78 (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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51A SER* 4.7 1.6 - - - +
74A TYR* 2.9 46.2 + - + +
75A LEU* 3.5 7.6 - - + +
76A LEU 3.2 0.2 - - - -
77A TYR* 1.3 96.9 - - + +
79A GLN* 1.3 62.2 + - - +
81A ARG* 2.9 24.9 - - - +
83A LEU* 3.1 37.3 + - + +
88A ILE* 4.0 24.9 - - + -
91A HIS* 3.5 40.2 - - + +
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Residues in contact with GLN 79 (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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75A LEU 3.0 15.0 + - - +
76A LEU* 3.2 16.7 + - - +
78A LEU* 1.3 71.1 - - - +
80A ALA* 1.3 54.3 + - - +
81A ARG 3.0 4.5 - - - -
82A GLY* 2.6 28.1 + - - -
83A LEU 3.6 3.8 + - - +
88A ILE* 3.7 18.1 - - + +
119A ARG* 5.3 1.2 + - - -
120A ILE* 3.5 35.2 + - + +
123A GLU* 3.5 24.9 + - - +
124A ASN* 3.0 32.4 + - - +
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Residues in contact with ALA 80 (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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76A LEU 2.8 17.8 + - - +
77A TYR* 3.7 8.1 - - - +
79A GLN* 1.3 72.5 - - - +
81A ARG* 1.3 56.5 + - - +
82A GLY* 2.8 10.3 + - - -
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Residues in contact with ARG 81 (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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77A TYR* 2.9 56.0 + - + +
78A LEU* 2.9 17.9 - - - +
79A GLN 3.0 0.2 - - - -
80A ALA* 1.3 76.3 - - - +
82A GLY* 1.3 63.9 + - - +
83A LEU* 3.7 26.5 - - + +
91A HIS* 6.2 0.2 - - - -
10D T 5.2 0.2 - - - -
11D A 2.6 43.8 + - - -
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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