Contacts of the helix formed by residues 80 - 93 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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77D VAL* 5.0 1.7 - - - +
79D SER* 1.3 87.8 + - - +
81D ASP* 1.3 68.3 + - - -
82D GLY 3.1 3.3 + - - -
83D LEU* 3.4 9.5 + - - +
84D MET* 3.5 11.6 + - - +
107D SER* 5.0 7.1 + - - -
111D GLY* 4.3 4.1 - - - +
112D SER 4.6 6.5 - - - -
113D GLY 3.4 11.9 - - - -
114D ASN* 3.7 4.9 - - - -
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Residues in contact with ASP 81 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80D GLY* 1.3 72.2 - - - -
82D GLY* 1.3 61.7 + - - +
84D MET* 3.3 9.0 + - - +
85D HIS* 3.1 22.2 + - - +
107D SER* 5.2 1.4 + - - -
112D SER 5.0 0.4 + - - -
113D GLY* 2.9 25.8 + - - +
114D ASN* 3.6 2.8 - - - -
115D ALA* 2.7 29.4 + - - +
116D LEU* 3.0 32.0 + - + +
117D ALA 4.5 0.3 + - - -
166D VAL* 5.0 3.6 - - + +
167D LEU* 3.6 19.5 - - + +
341D ASP* 3.9 18.3 - - + +
342D GLY* 5.8 0.4 - - - -
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Residues in contact with GLY 82 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80D GLY* 3.1 1.8 - - - -
81D ASP* 1.3 79.1 - - - +
83D LEU* 1.3 58.8 - - - +
85D HIS* 3.2 9.1 + - - +
86D GLU* 3.2 26.8 + - - +
112D SER 5.9 0.4 + - - -
341D ASP 4.0 11.1 + - - -
343D GLU* 5.7 7.0 - - - -
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Residues in contact with LEU 83 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20D LEU* 4.3 13.5 - - + +
22D ASN* 5.0 5.4 - - + +
54D THR* 4.0 29.4 - - + +
60D ALA* 3.7 26.5 - - + -
77D VAL* 3.3 27.8 - - + -
79D SER* 3.6 31.6 + - - +
80D GLY* 3.4 4.3 + - - +
81D ASP 3.3 0.2 - - - -
82D GLY* 1.3 73.2 - - - +
84D MET* 1.3 65.3 + - - +
86D GLU* 3.0 15.9 + - + +
87D VAL* 3.0 27.7 + - + +
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Residues in contact with MET 84 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77D VAL* 3.7 24.3 - - + +
80D GLY 3.5 9.7 + - - +
81D ASP* 3.3 10.4 + - - +
83D LEU* 1.3 77.2 - - - +
85D HIS* 1.3 62.6 + - - +
87D VAL* 3.2 4.9 + - - +
88D VAL* 2.9 29.3 + - + +
105D LEU* 4.1 24.9 - - + -
106D CYS 3.7 37.9 - - - +
107D SER* 3.8 17.9 - - - +
116D LEU* 3.6 23.6 - - + -
166D VAL* 4.2 9.6 - - + -
359D PHE* 5.4 1.3 - - + -
361D MET* 4.2 10.8 - - - +
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Residues in contact with HIS 85 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61D ARG* 4.7 5.6 - - - -
81D ASP 3.1 13.0 + - - +
82D GLY* 3.2 13.8 + - - +
84D MET* 1.3 76.9 - - - +
86D GLU* 1.3 72.7 + - - +
88D VAL* 4.0 3.2 - - - +
89D ASN* 3.0 47.8 + - - +
163D LEU* 4.0 14.5 - - + +
164D PHE 2.9 25.5 + - - -
165D SER* 4.2 0.2 - - - -
166D VAL* 4.6 5.7 - - + +
340D VAL* 3.8 18.2 + - + +
341D ASP* 2.8 41.1 - - + +
343D GLU* 5.4 12.7 - - + +
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Residues in contact with GLU 86 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58D ASN* 3.7 17.5 - - - +
60D ALA* 4.6 1.1 - - + -
61D ARG* 2.9 66.0 + - - +
82D GLY 3.2 13.9 + - - +
83D LEU* 3.0 24.6 + - + +
85D HIS* 1.3 83.6 + - - +
87D VAL* 1.3 56.1 + - - +
89D ASN 3.5 0.5 + - - -
90D GLY* 2.8 31.5 + - - -
343D GLU* 3.8 19.2 - - - +
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Residues in contact with VAL 87 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20D LEU* 3.9 16.4 - - + -
60D ALA* 4.7 4.9 - - + -
64D VAL* 3.3 36.9 - - + +
75D LEU* 4.3 10.8 - - + -
77D VAL* 4.2 21.3 - - + -
83D LEU* 3.0 19.8 + - + +
84D MET* 3.7 9.2 - - - +
86D GLU* 1.3 76.0 - - - +
88D VAL* 1.3 57.4 + - - +
90D GLY* 3.0 3.3 + - - -
91D LEU* 2.8 41.2 + - + +
105D LEU* 4.4 13.9 - - + -
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Residues in contact with VAL 88 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84D MET* 2.9 22.5 + - - +
85D HIS 4.1 1.8 - - - +
87D VAL* 1.3 74.6 - - - +
89D ASN* 1.3 62.7 + - - +
91D LEU* 3.2 9.3 + - - +
92D MET* 3.0 25.7 + - + +
101D ILE* 4.2 14.1 - - + -
105D LEU* 3.8 26.2 - - + -
152D LEU* 4.0 22.2 - - + -
164D PHE* 4.5 5.2 - - + -
166D VAL* 3.6 33.2 - - + -
359D PHE* 4.6 7.9 - - + -
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Residues in contact with ASN 89 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61D ARG* 3.6 28.8 - - - +
85D HIS* 3.0 36.6 + - - +
86D GLU 4.0 1.3 - - - +
88D VAL* 1.3 76.8 - - - +
90D GLY* 1.3 61.7 + - - +
92D MET* 3.6 4.3 + - - +
93D GLU* 3.2 32.1 + - - +
162D ARG 5.2 0.2 + - - -
163D LEU* 3.7 10.1 - - - +
164D PHE* 2.8 60.2 - - - +
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Residues in contact with GLY 90 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61D ARG* 3.8 26.2 - - - +
64D VAL* 3.9 7.2 - - - -
65D ARG* 4.0 6.1 - - - -
86D GLU 2.8 19.9 + - - -
87D VAL 3.0 4.7 + - - -
89D ASN* 1.3 71.9 - - - +
91D LEU* 1.3 64.7 + - - +
93D GLU* 3.3 15.7 + - - +
94D ARG* 3.7 12.8 - - - +
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Residues in contact with LEU 91 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64D VAL* 3.4 23.1 - - + +
69D LEU* 3.9 36.3 - - + -
75D LEU* 4.4 3.1 - - + -
87D VAL* 2.8 21.2 + - + +
88D VAL* 3.2 5.6 + - - +
90D GLY* 1.3 71.6 - - - +
92D MET* 1.3 63.1 + - - +
94D ARG* 3.3 24.8 + - - +
97D TRP* 3.8 4.1 - - - -
100D ALA* 3.7 26.4 - - + +
101D ILE* 4.1 19.7 - - + +
103D LYS* 5.1 1.6 - - + +
105D LEU* 4.0 37.7 - - + -
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Residues in contact with MET 92 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88D VAL* 3.0 21.5 + - + +
89D ASN 4.0 3.1 - - - +
91D LEU* 1.3 72.0 - - - +
93D GLU* 1.3 58.8 + - + +
94D ARG 3.0 10.7 + - - +
97D TRP* 3.2 35.2 - - + +
101D ILE* 3.7 39.5 - - + -
152D LEU* 4.2 11.7 - - + -
164D PHE* 3.6 56.0 - - + -
231D GLN 5.9 0.7 + - - -
232D GLY* 4.9 5.5 + - - -
233D PRO* 3.7 24.0 - - + -
358D TYR* 4.6 3.4 - - + -
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Residues in contact with GLU 93 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61D ARG* 3.0 38.7 + - - -
65D ARG* 2.7 44.7 + - - -
89D ASN* 3.2 24.3 + - - +
90D GLY 3.7 5.8 - - - +
91D LEU 3.2 1.0 - - - -
92D MET* 1.3 74.8 - - + +
94D ARG* 1.3 61.7 + - - +
95D PRO* 3.9 3.3 - - - +
164D PHE* 6.4 1.8 - - + -
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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