Contacts of the helix formed by residues 77 - 87 (chain F) in PDB entry 1VYH
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 THR 77 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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75F GLY 3.7 8.7 - - - +
76F ASP* 1.3 80.1 - - - +
78F THR* 1.3 66.9 + - - +
79F ARG* 3.3 21.3 + - - +
80F HIS* 2.9 34.9 + - + +
81F VAL* 3.0 13.0 + - - +
102F VAL* 3.9 5.2 - - - -
105F ASN* 4.1 15.9 - - - +
106F ASN* 3.6 22.4 - - - +
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Residues in contact with THR 78 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9F ALA* 2.9 28.4 + - - +
77F THR* 1.3 73.2 - - - +
79F ARG* 1.3 61.8 + - - +
81F VAL* 4.0 0.5 - - - +
82F LEU* 2.9 29.3 + - - +
102F VAL* 4.1 22.2 - - + -
103F GLY* 4.3 3.4 - - - -
106F ASN* 2.8 29.3 + - - +
114F VAL* 4.5 4.0 - - + +
117F GLY* 4.3 9.0 - - - -
118F ILE* 4.3 22.9 - - + +
121F ILE* 4.1 10.6 - - + +
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Residues in contact with ARG 79 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8F PRO* 2.5 37.3 + - - +
9F ALA* 3.7 15.7 + - - +
11F ILE* 3.1 29.9 + - - +
12F PRO* 3.4 3.2 - - - +
13F HIS* 3.2 72.8 + - - +
77F THR* 3.2 10.3 + - - +
78F THR* 1.3 83.7 + - - +
80F HIS* 1.3 58.9 + - - +
82F LEU* 3.6 3.0 - - - +
83F TRP 3.3 10.2 + - - -
106F ASN* 5.2 1.6 - - - +
108F GLU* 5.3 6.9 + - - -
109F ASN* 5.3 4.0 - - - +
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Residues in contact with HIS 80 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13F HIS* 3.1 43.6 - + - -
14F ALA* 4.5 0.2 - - - -
15F ALA* 3.4 37.3 - - + +
24F TRP* 4.3 4.7 - + + -
75F GLY 4.6 4.9 - - - -
76F ASP* 3.4 28.5 + - - +
77F THR* 2.9 39.8 + - + +
79F ARG* 1.3 72.7 - - - +
81F VAL* 1.3 67.2 + - - +
82F LEU 3.1 1.3 - - - -
83F TRP* 3.0 4.7 + - - +
84F ARG* 2.9 25.9 + - - +
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Residues in contact with VAL 81 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45F VAL* 5.0 10.5 - - + -
46F GLY* 3.9 22.7 - - - +
76F ASP* 3.6 16.6 + - + +
77F THR 3.0 9.1 + - - +
78F THR 4.0 2.7 - - - +
80F HIS* 1.3 74.9 - - - +
82F LEU* 1.3 71.9 + - - +
84F ARG* 3.4 19.1 + - - +
85F LEU* 3.0 40.1 + - + +
102F VAL* 3.9 17.9 - - + -
121F ILE* 3.7 20.4 - - + -
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Residues in contact with LEU 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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9F ALA 4.5 2.0 - - - +
10F ALA* 3.5 38.1 - - - +
11F ILE 4.7 0.2 - - - -
12F PRO* 4.1 14.1 - - + -
78F THR 2.9 17.8 + - - +
79F ARG 3.6 4.7 - - - +
81F VAL* 1.3 77.5 - - - +
83F TRP* 1.3 65.0 + - - +
85F LEU* 2.8 7.6 + - - +
86F LYS* 2.7 32.3 + - + +
117F GLY 4.9 1.6 - - - +
120F ALA* 4.4 14.6 - - + +
121F ILE* 3.6 31.2 - - + +
124F LEU* 3.9 24.7 - - + -
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Residues in contact with TRP 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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12F PRO* 3.8 14.7 - - + +
13F HIS* 3.6 26.7 - - - +
14F ALA* 3.6 31.2 - - + +
24F TRP* 3.5 31.4 - + - -
25F MET* 4.0 20.6 - - + -
28F HIS* 3.8 24.7 - + - -
79F ARG 3.3 2.6 + - - +
80F HIS 3.0 8.4 + - - +
82F LEU* 1.3 77.7 - - - +
84F ARG* 1.3 60.3 + - - +
86F LYS* 3.0 4.2 + - + -
87F ASN* 2.5 66.6 + - + +
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Residues in contact with ARG 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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24F TRP* 3.6 27.4 - - + -
28F HIS* 4.1 9.1 - - - +
31F PHE* 3.8 6.1 - - - -
45F VAL* 6.0 1.6 - - - +
46F GLY 3.3 18.4 + - - +
71F PHE* 2.8 29.9 + - - +
73F ILE* 3.4 27.3 - - - +
76F ASP* 2.9 26.4 + - - -
80F HIS 2.9 16.5 + - - +
81F VAL* 3.5 17.1 - - + +
83F TRP* 1.3 83.7 - - - +
85F LEU* 1.3 62.0 + - + +
87F ASN 3.3 10.4 + - - +
89F GLU* 2.8 64.3 + - - +
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Residues in contact with LEU 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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45F VAL* 4.1 25.4 - - + -
81F VAL* 3.0 37.2 + - + +
82F LEU* 2.8 9.9 + - - +
84F ARG* 1.3 71.6 - - + +
86F LYS* 1.3 67.3 + - - +
88F GLY* 3.5 7.8 + - - -
89F GLU* 3.9 17.8 + - + +
90F LEU* 3.6 44.0 - - + +
98F ILE* 6.3 0.2 - - + -
121F ILE* 3.9 20.0 - - + -
124F LEU* 3.6 22.2 - - + +
125F ILE* 4.5 10.5 - - + -
128F ARG* 5.1 3.6 + - - -
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Residues in contact with LYS 86 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12F PRO* 4.5 26.8 - - + +
82F LEU* 2.7 19.2 + - + +
83F TRP* 3.4 11.7 - - + +
85F LEU* 1.3 79.6 - - - +
87F ASN* 1.3 67.2 + - - +
88F GLY 3.4 3.3 + - - -
124F LEU* 4.1 28.2 - - + +
128F ARG* 3.2 34.4 + - - +
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Residues in contact with ASN 87 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28F HIS* 3.5 18.5 + - - +
32F VAL* 4.3 3.5 - - - +
83F TRP* 2.5 80.6 + - + +
84F ARG 3.5 5.6 - - - +
85F LEU 3.2 0.4 - - - -
86F LYS* 1.3 84.3 - - - +
88F GLY* 1.3 56.9 + - - +
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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