Contacts of the helix formed by residues 81 - 92 (chain D) in PDB entry 2P5V
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 ASP 81 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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79D ALA 3.6 0.6 + - - -
80D LYS* 1.3 89.4 - - - +
82D ALA* 1.3 54.9 + - - +
83D ARG 3.4 2.5 - - - +
84D GLU* 3.9 16.7 - - + +
85D ASP* 2.7 52.5 + - - +
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Residues in contact with ALA 82 (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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76D ILE* 3.7 4.3 - - + +
77D ARG* 3.4 30.3 - - + +
79D ALA* 3.4 16.2 + - + +
80D LYS 3.1 4.5 - - - +
81D ASP* 1.3 77.8 - - - +
83D ARG* 1.3 58.2 + - + +
85D ASP* 3.9 4.2 - - - +
86D PHE* 2.9 32.9 + - - +
132D HIS* 5.4 3.1 - - + -
133D GLY* 4.0 25.2 - - - +
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Residues in contact with ARG 83 (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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143C LEU* 6.0 1.2 - - - +
76D ILE* 4.1 32.1 - - + +
77D ARG 5.6 0.4 - - - +
78D LYS* 5.6 0.8 - - - +
79D ALA 5.0 0.6 + - - +
81D ASP 3.4 0.4 - - - -
82D ALA* 1.3 78.3 - - + +
84D GLU* 1.3 68.0 + - - +
86D PHE* 3.8 1.6 - - - +
87D ALA* 2.9 29.5 + - - +
101D ALA* 4.2 7.5 - - - +
107D ASP* 4.3 19.4 + - - +
108D TYR* 3.1 43.0 + - - +
1014D CL 3.2 20.5 - - + +
125F LEU* 3.9 13.9 - - - +
129F LEU* 3.6 31.0 - - - +
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Residues in contact with GLU 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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144C LYS* 4.4 15.4 + - - -
81D ASP* 3.4 19.7 + - + +
82D ALA 3.4 0.4 - - - -
83D ARG* 1.3 85.2 - - - +
85D ASP* 1.3 67.9 - - - +
87D ALA* 3.2 10.3 + - - +
88D ALA* 2.9 24.7 + - - +
91D ARG* 4.9 0.9 + - - -
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Residues in contact with ASP 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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80D LYS 5.2 0.3 - - - +
81D ASP* 2.7 40.8 + - - +
82D ALA* 3.9 3.1 - - - +
84D GLU* 1.3 72.6 - - - +
86D PHE* 1.3 61.9 + - - +
88D ALA* 3.5 7.4 + - - +
89D SER* 3.1 26.5 + - - -
131D HIS* 3.5 3.1 + - + -
132D HIS* 2.6 40.5 + - + +
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Residues in contact with PHE 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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74D VAL* 3.8 15.3 - - + -
76D ILE* 3.5 19.7 - - + -
82D ALA 2.9 20.2 + - - +
83D ARG 3.8 1.1 - - - +
85D ASP* 1.3 72.7 - - - +
87D ALA* 1.3 69.8 + - - +
89D SER* 3.2 1.4 + - - -
90D VAL* 3.0 51.4 + - + +
93D TRP* 4.1 6.1 - + - -
99D CYS* 4.3 6.1 - - - -
108D TYR* 4.0 35.9 - + + -
110D LEU* 4.2 13.7 - - + -
128D LEU* 4.0 10.5 - - + -
131D HIS* 3.6 18.1 - + + -
133D GLY 5.1 0.2 - - - +
134D VAL* 3.6 30.5 - - + -
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Residues in contact with ALA 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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146C ILE* 3.6 33.4 - - + +
83D ARG 2.9 14.9 + - - +
84D GLU* 3.3 16.8 - - - +
86D PHE* 1.3 80.1 - - - +
88D ALA* 1.3 62.0 - - - +
90D VAL* 3.4 2.6 + - - +
91D ARG* 3.2 46.3 + - - +
108D TYR* 5.6 1.1 - - + +
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Residues in contact with ALA 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 GLU 2.9 15.9 + - - +
85D ASP* 3.7 7.9 - - - +
86D PHE 3.2 0.2 - - - -
87D ALA* 1.3 77.8 - - - +
89D SER* 1.3 62.8 + - - +
91D ARG* 3.6 21.0 + - - +
92D LYS* 3.5 26.6 + - - +
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Residues in contact with SER 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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85D ASP 3.1 8.5 + - - -
86D PHE 3.2 3.1 + - - -
88D ALA* 1.3 73.8 - - - +
90D VAL* 1.3 60.1 + - - +
92D LYS* 2.9 36.1 + - - +
93D TRP* 3.4 31.2 + - - +
131D HIS* 2.8 40.4 + - - -
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Residues in contact with VAL 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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146C ILE* 4.5 3.4 - - + -
147C LYS* 2.8 36.7 + - + -
86D PHE* 3.0 51.3 + - + +
87D ALA 3.8 4.3 - - - +
89D SER* 1.3 77.0 - - - +
91D ARG* 1.3 58.5 + - - +
93D TRP* 3.2 30.7 + - + +
96D VAL* 4.0 9.8 - - + +
99D CYS* 3.6 29.8 - - + -
110D LEU* 4.3 6.7 - - + -
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Residues in contact with ARG 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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144C LYS* 6.2 0.6 - - - +
145C GLU 5.2 0.6 + - - -
146C ILE* 3.1 46.9 + - + +
147C LYS* 3.5 25.7 + - + -
84D GLU 4.9 0.8 + - - -
87D ALA* 3.2 33.9 + - - +
88D ALA* 3.7 17.0 - - - +
89D SER 3.2 0.8 - - - -
90D VAL* 1.3 76.0 - - - +
92D LYS* 1.3 59.6 + - + +
93D TRP 3.5 0.2 - - - -
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Residues in contact with LYS 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 ALA* 3.5 22.6 + - - +
89D SER* 2.9 21.3 + - - +
91D ARG* 1.3 79.9 - - + +
93D TRP* 1.3 65.2 + - + +
94D PRO* 3.4 10.7 - - - +
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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