Contacts of the helix formed by residues 80 - 93 (chain F) in PDB entry 3VZC
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 GLY 80 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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77F VAL* 4.3 5.7 - - - +
79F SER* 1.3 87.2 + - - +
81F ASP* 1.3 64.3 + - - -
82F GLY 3.2 4.0 + - - +
83F LEU* 3.8 8.3 + - - +
84F MET* 4.2 6.1 + - - +
107F SER* 5.2 4.0 + - - -
112F SER 4.0 8.1 - - - -
113F GLY 3.6 13.7 - - - -
114F ASN* 3.8 8.6 - - - +
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Residues in contact with ASP 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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80F GLY* 1.3 72.9 - - - +
82F GLY* 1.3 64.8 + - - +
83F LEU 3.2 0.9 - - - -
84F MET* 3.2 10.0 + - - +
85F HIS* 3.1 22.2 + - - +
113F GLY* 3.1 14.3 + - - +
114F ASN* 3.6 5.4 - - - +
115F ALA* 2.9 30.0 + - - +
116F LEU* 3.1 34.6 + - + +
117F ALA 4.3 0.3 + - - -
166F VAL* 5.0 2.8 - - + +
167F LEU* 3.7 16.4 - - + +
268F LEU 4.9 0.5 - - - +
341F ASP* 3.9 18.6 - - + +
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Residues in contact with GLY 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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80F GLY* 3.2 2.4 - - - -
81F ASP* 1.3 79.3 - - - +
83F LEU* 1.3 60.2 + - - +
85F HIS* 3.5 5.2 - - - +
86F GLU* 3.3 26.0 + - - +
341F ASP 3.8 9.2 + - - -
342F GLY 5.9 0.2 - - - -
343F GLU* 3.6 29.9 - - - -
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Residues in contact with LEU 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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20F LEU* 3.6 33.9 - - + +
22F ASN* 4.4 2.9 - - + +
54F THR* 4.2 19.5 - - + +
60F ALA* 3.2 34.3 - - + -
77F VAL* 3.5 19.1 - - + -
79F SER* 3.6 32.6 + - - +
80F GLY 3.8 2.4 + - - +
81F ASP 3.2 0.6 - - - -
82F GLY* 1.3 75.0 - - - +
84F MET* 1.3 59.1 + - - +
86F GLU* 3.1 10.7 + - + +
87F VAL* 3.0 32.9 + - + +
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Residues in contact with MET 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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77F VAL* 3.7 23.4 - - + +
80F GLY 4.8 0.7 - - - +
81F ASP* 3.2 14.2 + - - +
83F LEU* 1.3 73.6 - - - +
85F HIS* 1.3 67.9 + - - +
87F VAL* 3.1 5.9 + - - +
88F VAL* 2.9 29.6 + - + +
105F LEU* 3.9 31.0 - - + -
106F CYS 3.2 31.0 - - - +
107F SER* 3.5 23.6 - - - +
116F LEU* 3.6 26.2 - - + -
166F VAL* 4.2 10.5 - - + -
361F MET* 4.3 7.6 - - + +
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Residues in contact with HIS 85 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61F ARG* 4.5 11.0 - - - -
81F ASP 3.1 10.2 + - - +
82F GLY* 3.5 11.0 - - - +
84F MET* 1.3 78.0 - - - +
86F GLU* 1.3 76.8 + - - +
88F VAL* 3.4 3.6 + - - +
89F ASN* 2.9 45.8 + - - +
163F LEU* 3.8 11.6 - - + +
164F PHE 3.4 20.1 + - - -
166F VAL* 4.5 5.0 - - - +
340F VAL* 3.8 24.6 + - + +
341F ASP* 2.8 41.3 - - + +
343F GLU* 4.5 8.9 - - + +
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Residues in contact with GLU 86 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57F ARG* 5.8 0.9 - - - +
58F ASN* 3.2 27.2 + - - +
59F HIS 5.8 0.2 - - - +
60F ALA* 4.4 7.2 - - + +
61F ARG* 3.2 59.5 + - + +
82F GLY 3.3 14.3 + - - +
83F LEU* 3.1 13.7 + - + +
85F HIS* 1.3 90.2 + - - +
87F VAL* 1.3 58.2 + - - +
89F ASN* 3.5 2.7 + - - +
90F GLY* 2.9 24.6 + - - -
343F GLU* 3.3 21.4 - - - +
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Residues in contact with VAL 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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20F LEU* 3.6 28.9 - - + -
60F ALA* 4.4 6.3 - - + -
61F ARG* 5.0 0.4 - - - +
64F VAL* 3.7 22.8 - - + +
75F LEU* 4.1 19.7 - - + -
77F VAL* 3.7 17.5 - - + -
83F LEU* 3.0 19.8 + - + +
84F MET* 3.1 8.9 + - - +
86F GLU* 1.3 76.7 - - - +
88F VAL* 1.3 56.7 + - - +
90F GLY* 3.3 1.9 + - - -
91F LEU* 2.9 29.0 + - + +
105F LEU* 4.5 18.2 - - + -
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Residues in contact with VAL 88 (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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84F MET* 2.9 21.0 + - + +
85F HIS 4.0 2.2 - - - +
87F VAL* 1.3 73.6 - - - +
89F ASN* 1.3 62.6 + - - +
91F LEU* 3.2 8.5 + - - +
92F MET* 2.8 34.2 + - + +
101F ILE* 4.0 16.2 - - + -
105F LEU* 3.5 30.3 - - + -
152F LEU* 3.8 27.6 - - + -
164F PHE* 4.6 5.8 - - + -
166F VAL* 3.6 21.5 - - + -
359F PHE* 4.8 4.9 - - + -
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Residues in contact with ASN 89 (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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61F ARG* 3.3 29.0 - - - +
85F HIS* 2.9 38.2 + - - +
86F GLU 4.0 1.1 - - - +
88F VAL* 1.3 77.0 - - - +
90F GLY* 1.3 56.5 + - - +
92F MET* 3.4 5.8 + - - +
93F GLU* 3.1 36.9 + - - +
162F ARG 5.0 0.4 + - - -
163F LEU* 3.5 15.6 - - - +
164F PHE* 2.8 56.8 - - - +
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Residues in contact with GLY 90 (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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61F ARG* 3.7 21.9 - - - +
64F VAL* 4.4 0.7 - - - -
65F ARG* 3.6 15.4 - - - +
86F GLU 2.9 15.6 + - - -
87F VAL 3.6 4.5 - - - -
88F VAL 3.1 0.2 - - - -
89F ASN* 1.3 74.3 - - - +
91F LEU* 1.3 63.7 - - - +
93F GLU* 3.5 13.2 + - - -
94F ARG* 3.3 18.4 + - - +
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Residues in contact with LEU 91 (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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64F VAL* 3.7 17.2 - - + +
69F LEU* 3.7 18.6 - - + -
75F LEU* 4.7 4.0 - - + -
87F VAL* 2.9 20.9 + - + +
88F VAL* 3.4 7.6 - - - +
90F GLY* 1.3 75.8 - - - +
92F MET* 1.3 62.6 + - - +
93F GLU 3.2 1.2 + - - -
94F ARG* 3.3 22.1 + - - +
97F TRP* 3.6 11.6 - - - +
100F ALA* 3.4 36.0 - - + +
101F ILE* 4.3 24.7 - - + +
103F LYS* 4.8 3.1 - - + +
105F LEU* 4.1 31.4 - - + -
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Residues in contact with MET 92 (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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88F VAL* 2.8 25.5 + - + +
89F ASN 3.4 3.6 + - - +
90F GLY 3.3 0.2 - - - -
91F LEU* 1.3 73.1 - - - +
93F GLU* 1.3 61.0 + - - +
94F ARG 3.3 0.6 - - - +
97F TRP* 3.4 33.7 - - + +
101F ILE* 3.8 38.1 - - + -
152F LEU* 4.8 1.6 - - + -
164F PHE* 3.5 60.3 - - + -
231F GLN 5.7 0.3 - - - +
233F PRO* 3.6 24.9 - - + -
358F TYR* 3.9 13.5 - - + -
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Residues in contact with GLU 93 (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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61F ARG* 2.4 45.9 + - - +
65F ARG* 3.0 46.2 + - - +
89F ASN* 3.1 17.7 + - - +
90F GLY* 3.8 2.0 - - - +
91F LEU 3.1 0.8 - - - -
92F MET* 1.3 76.9 - - - +
94F ARG* 1.3 65.4 + - - +
95F PRO* 3.8 2.6 - - - +
164F PHE* 6.5 0.7 - - + -
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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