Contacts of the helix formed by residues 75 - 87 (chain F) 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 F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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62E LYS* 3.9 17.7 - - - +
-5F LEU* 5.7 10.5 - - + -
73F ASP 4.6 1.3 - - - +
74F PRO* 1.3 86.7 - - + +
76F LEU* 1.3 66.2 + - - +
77F ASP* 3.4 16.2 - - - +
78F GLU* 3.3 15.3 + - + -
79F VAL* 3.2 20.8 + - - +
97F TYR* 3.7 21.8 - - + +
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Residues in contact with LEU 76 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36E ILE* 3.7 23.1 - - + +
40E GLY* 3.5 19.5 - - - +
43E LEU* 4.4 3.8 - - + -
58E SER* 3.7 31.9 - - - +
61E LEU* 3.4 34.3 - - + -
62E LYS* 4.8 14.0 - - + +
65E LEU* 3.8 14.6 - - + -
74F PRO 3.3 4.9 + - - -
75F PRO* 1.3 71.2 - - - +
77F ASP* 1.3 65.7 + - - +
80F LEU* 3.0 23.6 + - + +
90F PHE* 3.6 21.4 - - + -
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Residues in contact with ASP 77 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54E TRP* 5.3 1.6 - - - -
58E SER* 3.9 26.5 + - - +
59E ARG* 4.8 18.1 - - + +
62E LYS* 3.1 40.1 + - + +
75F PRO* 3.4 7.8 - - - +
76F LEU* 1.3 75.7 - - - +
78F GLU* 1.3 81.3 + - - +
80F LEU* 3.6 2.3 + - - +
81F ARG* 3.2 23.2 + - - +
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Residues in contact with GLU 78 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62E LYS* 5.7 0.2 - - - +
-7F GLU* 3.4 23.0 - - - +
75F PRO* 3.5 24.2 - - + +
76F LEU 3.2 0.4 - - - -
77F ASP* 1.3 89.4 + - - +
79F VAL* 1.3 68.4 + - - +
81F ARG* 3.3 28.0 + - - +
82F VAL* 3.2 23.7 + - - +
97F TYR* 3.3 37.7 + - + +
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Residues in contact with VAL 79 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37E TYR* 6.3 0.2 - - + -
74F PRO* 3.6 26.0 - - + +
75F PRO 3.2 14.4 + - - +
76F LEU 3.9 0.9 - - - +
78F GLU* 1.3 73.4 - - - +
80F LEU* 1.3 69.4 + - - +
82F VAL* 2.6 21.4 + - - +
83F ALA 2.9 9.5 + - - -
90F PHE* 3.5 37.0 - - + +
93F ALA* 3.5 5.6 - - + -
94F SER* 3.4 39.3 - - - +
97F TYR* 4.1 9.6 - - + -
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Residues in contact with LEU 80 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40E GLY 4.9 1.8 - - - +
43E LEU* 4.0 15.0 - - + -
44E TRP* 4.1 31.0 - - + +
47E ALA* 4.8 1.8 - - + -
54E TRP* 3.5 30.1 - - + +
58E SER* 3.6 24.2 - - - -
76F LEU* 3.0 16.9 + - + +
77F ASP 3.7 4.0 - - - +
79F VAL* 1.3 77.1 - - - +
81F ARG* 1.3 57.7 + - - +
83F ALA* 3.0 3.9 + - + +
84F VAL* 2.8 47.0 + - + +
90F PHE* 3.6 17.4 - - + -
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Residues in contact with ARG 81 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54E TRP* 4.0 26.6 - - + -
-10F PRO* 5.4 9.7 - - - +
-9F THR* 5.2 6.9 + - - -
77F ASP 3.2 11.7 + - - +
78F GLU* 3.5 27.5 + - - +
79F VAL 3.0 0.8 - - - -
80F LEU* 1.3 79.9 - - - +
82F VAL* 1.3 58.4 + - + +
84F VAL* 3.7 1.0 - - - +
85F GLU* 2.8 61.8 + - + +
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Residues in contact with VAL 82 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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-10F PRO* 4.3 19.1 - - + -
78F GLU 3.4 13.9 - - - +
79F VAL* 2.6 14.0 + - - +
81F ARG* 1.3 72.0 - - + +
83F ALA* 1.3 56.3 + - - +
85F GLU* 4.3 11.0 - - - +
86F ARG* 2.8 65.2 + - + +
88F LEU* 4.9 1.6 - - + -
93F ALA* 4.2 19.7 - - + +
96F ALA* 4.8 5.6 - - + -
97F TYR* 4.1 25.4 - - + +
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Residues in contact with ALA 83 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44E TRP* 3.8 18.0 + - + -
79F VAL 2.9 7.2 + - - +
80F LEU* 3.4 10.3 - - - +
82F VAL* 1.3 77.3 - - - +
84F VAL* 1.3 54.8 + - - +
87F GLY* 2.8 31.4 + - - -
88F LEU* 3.0 30.8 + - - +
89F THR 3.8 4.9 - - - +
90F PHE* 4.2 5.2 - - - -
93F ALA* 3.6 20.3 - - + +
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Residues in contact with VAL 84 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44E TRP* 4.6 7.4 - - + +
47E ALA* 4.3 12.3 - - + -
54E TRP* 3.7 40.2 - - + +
80F LEU* 2.8 39.7 + - + +
81F ARG 3.7 3.4 - - - +
83F ALA* 1.3 76.7 - - - +
85F GLU* 1.3 64.9 + - + +
87F GLY* 3.8 5.7 + - - -
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Residues in contact with GLU 85 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54E TRP* 6.1 0.7 - - + -
-10F PRO* 5.7 3.6 - - - +
81F ARG* 2.8 59.2 + - + +
82F VAL* 3.9 9.4 - - - +
84F VAL* 1.3 78.6 - - + +
86F ARG* 1.3 67.7 + - + +
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Residues in contact with ARG 86 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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-10F PRO* 4.4 16.6 - - - +
82F VAL* 2.8 43.1 + - + +
85F GLU* 1.3 83.7 + - + +
87F GLY* 1.3 51.9 + - - +
88F LEU* 4.1 16.8 - - + -
96F ALA* 4.3 8.8 - - - +
100F GLU* 2.7 38.8 + - - -
116F LYS* 2.5 78.7 + - + +
117F THR* 4.2 1.2 - - - +
118F LYS* 5.1 9.9 - - - +
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Residues in contact with GLY 87 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44E TRP* 5.8 1.3 - - - -
48E ARG* 5.2 9.5 + - - -
83F ALA 2.8 15.2 + - - -
84F VAL 3.8 4.0 + - - -
85F GLU 3.6 2.0 - - - -
86F ARG* 1.3 74.6 - - - +
88F LEU* 1.3 58.8 + - - +
112F GLU* 5.5 1.2 - - - +
116F LYS* 3.2 15.5 + - - -
87G GLY 5.3 2.8 - - - +
112G GLU* 4.0 27.3 - - - +
48H ARG* 5.8 1.6 + - - -
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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