Contacts of the helix formed by residues 75 - 87 (chain H) in PDB entry 1V8P
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 PRO 75 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62G LYS* 3.8 31.6 - - + +
73H ASP 4.6 1.1 - - - +
74H PRO* 1.3 84.4 - - + +
76H LEU* 1.3 62.7 + - - +
77H ASP* 2.8 6.6 + - + -
78H GLU* 3.0 27.1 + - + -
79H VAL* 3.2 12.4 + - - +
97H TYR* 3.9 20.2 - - + +
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Residues in contact with LEU 76 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36G ILE* 3.8 14.5 - - + +
40G GLY* 3.8 14.8 - - - -
43G LEU* 4.5 4.5 - - + -
58G SER* 3.9 28.9 - - - +
61G LEU* 3.4 33.9 - - + -
62G LYS* 4.7 14.1 - - + +
65G LEU* 3.5 24.7 - - + -
74H PRO 3.3 5.6 + - - -
75H PRO* 1.3 70.1 - - - +
77H ASP* 1.3 62.9 + - - +
79H VAL* 4.0 0.4 - - - -
80H LEU* 3.1 23.0 + - + +
90H PHE* 3.6 29.1 - - + -
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Residues in contact with ASP 77 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54G TRP* 5.6 1.0 - - - -
58G SER* 3.2 26.9 + - - -
59G ARG* 3.3 26.6 + - - +
62G LYS* 3.9 30.4 + - + +
75H PRO* 2.8 9.4 - - + -
76H LEU* 1.3 80.9 - - - +
78H GLU* 1.3 72.5 + - + +
80H LEU* 3.5 9.4 + - - +
81H ARG* 3.6 11.3 + - - +
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Residues in contact with GLU 78 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75H PRO* 3.0 24.8 + - + +
77H ASP* 1.3 87.6 - - + +
79H VAL* 1.3 65.1 + - - +
81H ARG* 3.1 31.4 + - - +
82H VAL* 3.1 17.5 + - - +
97H TYR* 3.0 45.1 + - + +
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Residues in contact with VAL 79 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37G TYR* 6.4 0.2 - - + -
74H PRO* 3.5 26.9 - - + -
75H PRO 3.2 15.8 + - - +
76H LEU 3.9 0.9 - - - +
78H GLU* 1.3 74.5 - - - +
80H LEU* 1.3 63.9 + - - +
82H VAL* 3.1 10.3 + - - +
83H ALA* 2.9 20.8 + - - +
90H PHE* 3.5 36.6 - - + +
93H ALA* 3.8 2.8 - - + +
94H SER* 3.3 40.8 - - - +
97H TYR* 4.4 8.7 - - + -
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Residues in contact with LEU 80 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40G GLY 4.9 0.9 - - - +
43G LEU* 3.7 24.5 - - + +
44G TRP* 3.8 35.9 - - + +
47G ALA* 4.8 1.6 - - + -
54G TRP* 3.7 21.5 - - + +
58G SER* 3.6 26.7 - - - -
76H LEU* 3.1 17.2 + - + +
77H ASP 3.7 5.2 - - - +
79H VAL* 1.3 77.5 - - - +
81H ARG* 1.3 58.6 + - - +
83H ALA* 3.2 2.0 + - - -
84H VAL* 2.9 48.9 + - + +
90H PHE* 3.9 13.9 - - + -
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Residues in contact with ARG 81 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54G TRP* 4.2 23.5 - - + -
77H ASP 3.6 7.2 + - - +
78H GLU* 3.1 25.6 + - - +
80H LEU* 1.3 80.2 - - - +
82H VAL* 1.3 67.8 + - - +
84H VAL* 3.2 2.1 + - - +
85H GLU* 2.9 69.3 + - - +
97H TYR* 6.1 3.0 - - - -
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Residues in contact with VAL 82 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78H GLU 3.3 13.7 - - - +
79H VAL* 3.1 7.5 + - - +
81H ARG* 1.3 88.6 - - + +
83H ALA* 1.3 56.7 + - - +
85H GLU* 4.4 6.7 - - - -
86H ARG* 2.9 65.7 + - - +
88H LEU* 4.8 1.7 - - + +
93H ALA* 4.0 22.2 - - + +
96H ALA* 4.6 6.7 - - + -
97H TYR* 3.8 28.9 - - + +
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Residues in contact with ALA 83 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44G TRP* 3.7 18.3 + - + -
79H VAL 2.9 12.7 + - - +
80H LEU* 3.5 9.9 - - - +
82H VAL* 1.3 77.5 - - - +
84H VAL* 1.3 63.6 + - - +
87H GLY* 3.1 5.4 + - - -
88H LEU* 3.1 43.4 + - - +
89H THR 4.1 4.9 - - - +
90H PHE* 4.2 4.5 - - - +
93H ALA* 3.6 18.1 - - + +
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Residues in contact with VAL 84 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112E GLU* 5.2 2.6 - - - +
44G TRP* 4.8 5.2 - - + +
47G ALA* 4.5 11.9 - - + -
54G TRP* 3.9 41.5 - - + +
80H LEU* 2.9 44.6 + - + +
81H ARG 3.7 3.6 - - - +
83H ALA* 1.3 79.4 - - - +
85H GLU* 1.3 64.6 + - + +
87H GLY* 3.8 5.7 + - - -
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Residues in contact with GLU 85 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54G TRP* 6.2 0.9 - - + -
81H ARG* 2.9 62.4 + - + +
82H VAL* 4.1 5.5 - - - +
84H VAL* 1.3 82.4 - - + +
86H ARG* 1.3 67.2 + - + +
87H GLY 3.6 0.5 + - - -
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Residues in contact with ARG 86 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82H VAL* 2.9 41.5 + - - +
85H GLU* 1.3 82.9 + - + +
87H GLY* 1.3 55.6 + - - +
88H LEU* 3.3 14.8 + - + -
96H ALA* 4.5 8.6 - - - +
100H GLU* 2.6 44.6 + - - -
116H LYS* 2.7 71.3 + - + +
117H THR* 4.3 0.8 - - - +
118H LYS* 3.6 15.5 - - - +
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Residues in contact with GLY 87 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87E GLY 5.2 1.2 - - - +
112E GLU* 3.9 32.1 - - - +
116E LYS* 5.7 0.2 + - - -
1001E CL 3.9 17.2 - - - +
48G ARG* 5.5 4.9 - - - -
83H ALA 3.1 8.2 + - - -
84H VAL 3.8 3.4 + - - -
85H GLU 3.4 4.9 + - - -
86H ARG* 1.3 78.9 - - - +
88H LEU* 1.3 62.4 + - - +
112H GLU* 4.8 3.1 - - - +
116H LYS* 3.8 9.5 + - - -
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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
------------------------------------------------------------
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