Contacts of the helix formed by residues 67 - 78 (chain A) in PDB entry 1POP
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 TYR 67 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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26A TRP* 3.9 11.4 - - - +
59A ARG* 3.8 26.0 - - + -
60A SER* 2.9 11.4 + - - -
61A TYR* 4.6 5.6 - + - -
66A GLY* 1.3 77.0 - - - -
68A PRO* 1.4 67.9 - - - +
69A TRP* 3.6 44.2 - + + +
70A SER* 3.2 24.9 + - - +
71A ALA 3.2 9.5 + - - -
423A MOH 5.1 1.1 - - - -
300B ACE 3.4 26.1 + - - +
301B LEU* 3.1 29.8 - - + +
302B LEU* 4.5 4.9 - - + -
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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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26A TRP* 4.0 19.7 - - + +
30A ALA* 4.2 1.7 - - + +
66A GLY 4.0 1.6 - - - +
67A TYR* 1.4 82.0 - - - +
69A TRP* 1.3 61.2 + - - +
71A ALA* 3.3 4.0 + - + +
72A LEU* 3.0 29.9 + - + +
131A SER* 3.4 23.6 - - - +
133A VAL* 4.9 2.9 - - + -
160A ALA* 3.6 29.8 - - + -
207A PHE* 5.4 2.7 - - + -
423A MOH 3.3 25.1 - - - +
302B LEU* 3.9 15.0 - - + -
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Residues in contact with TRP 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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59A ARG* 4.2 18.4 - - - -
67A TYR* 3.6 41.3 - + + +
68A PRO* 1.3 76.2 - - - +
70A SER* 1.3 85.6 + - - +
72A LEU* 3.3 11.5 + - - +
73A GLN* 2.9 43.3 + - - +
110A VAL* 4.8 6.9 - - + +
207A PHE* 4.0 37.4 - + + -
423A MOH 3.3 30.0 - - - -
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Residues in contact with SER 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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57A ASP* 3.3 21.3 - - - -
59A ARG* 2.9 45.5 + - - +
60A SER* 4.7 0.2 - - - -
67A TYR* 3.2 14.9 + - - +
69A TRP* 1.3 94.1 - - - +
71A ALA* 1.3 65.2 + - - +
73A GLN* 3.2 1.0 + - - -
74A LEU* 2.9 24.8 + - - +
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Residues in contact with ALA 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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26A TRP* 4.1 17.9 - - + +
30A ALA* 3.8 10.3 - - + -
53A LEU* 3.7 28.7 - - + +
57A ASP* 3.4 6.2 + - - -
67A TYR 3.2 10.0 + - - +
68A PRO 3.3 8.3 + - - +
70A SER* 1.3 78.1 - - - +
72A LEU* 1.3 63.0 + - - +
74A LEU* 3.4 7.6 - - - +
75A VAL* 3.2 28.4 + - - +
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Residues in contact with LEU 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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30A ALA* 4.0 16.2 - - + -
33A THR* 3.5 25.6 - - - +
34A ILE* 4.0 17.7 - - + -
68A PRO 3.0 22.9 + - - +
69A TRP 3.6 4.3 - - - +
71A ALA* 1.3 78.1 - - - +
73A GLN* 1.3 59.9 + - - +
75A VAL* 3.2 13.7 + - + +
76A ALA* 3.3 13.0 + - - +
107A THR* 4.3 2.8 + - - -
109A GLY 5.3 0.5 - - - +
110A VAL* 4.0 21.0 - - + +
131A SER* 4.6 8.1 - - - -
207A PHE* 4.0 35.2 - - + +
208A TYR 4.5 2.9 - - - +
209A PRO* 4.2 13.7 - - + +
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Residues in contact with GLN 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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59A ARG* 3.0 33.4 + - - +
69A TRP* 2.9 30.2 + - - +
70A SER 3.7 3.8 - - - +
72A LEU* 1.3 72.0 - - - +
74A LEU* 1.3 60.5 + - - +
76A ALA* 2.9 10.1 + - + +
77A GLN* 2.8 50.4 + - + +
110A VAL* 4.4 17.1 - - + +
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Residues in contact with LEU 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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53A LEU* 4.8 12.8 - - + -
56A CYS* 4.3 31.4 - - + +
57A ASP* 4.4 17.7 - - + +
58A ARG 6.0 0.2 - - - +
59A ARG* 4.5 7.4 - - - +
70A SER 2.9 11.3 + - - +
71A ALA* 3.4 13.7 - - - +
73A GLN* 1.3 75.3 - - - +
75A VAL* 1.3 56.5 + - - +
77A GLN* 3.2 3.0 + - - +
78A TYR* 2.9 63.3 + - + +
79A GLY 3.6 7.4 + - - +
424A MOH 4.1 16.8 - - - -
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Residues in contact with VAL 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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34A ILE* 3.6 34.3 - - + -
53A LEU* 3.8 20.0 - - + -
71A ALA 3.2 15.5 + - - +
72A LEU* 3.2 7.8 + - + +
73A GLN 3.2 0.6 - - - -
74A LEU* 1.3 75.1 - - - +
76A ALA* 1.3 58.9 + - - +
79A GLY* 3.3 25.6 + - - +
80A ILE* 3.9 29.8 - - + -
105A ALA* 4.7 2.2 - - + +
106A LYS* 3.8 1.7 - - - +
107A THR* 3.5 29.4 + - + +
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Residues in contact with ALA 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 LEU 3.3 8.9 + - - +
73A GLN* 2.9 12.9 + - + +
75A VAL* 1.3 77.4 - - - +
77A GLN* 1.3 62.8 + - + +
106A LYS* 3.3 17.0 - - - -
107A THR* 3.3 30.5 - - - +
108A ASP 4.7 0.7 - - - -
109A GLY* 3.9 23.3 - - - +
110A VAL* 5.6 0.7 - - + -
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Residues in contact with GLN 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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59A ARG* 4.4 0.2 + - - -
73A GLN* 2.8 44.7 + - + +
74A LEU* 4.1 4.3 + - - +
76A ALA* 1.3 78.5 - - + +
78A TYR* 1.3 80.0 + - + +
106A LYS* 3.3 14.9 + - - -
424A MOH 3.4 32.2 - - - -
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Residues in contact with TYR 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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74A LEU* 2.9 37.2 + - + +
75A VAL 4.1 1.3 - - - -
76A ALA 3.5 0.2 - - - -
77A GLN* 1.3 103.0 + - + +
79A GLY* 1.3 58.6 + - - +
103A TYR* 3.1 43.3 - + + +
106A LYS* 3.6 19.5 + - - +
424A MOH 3.5 25.4 + - - -
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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