Contacts of the helix formed by residues 83 - 91 (chain D) in PDB entry 2HVY
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 SER 83 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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21D LEU* 5.3 0.2 - - - +
55D ALA* 4.2 3.4 - - - -
57D ASP* 3.5 8.7 + - - -
81D VAL* 3.4 5.3 - - - +
82D PRO* 1.3 81.9 - - - +
84D LYS* 1.3 59.6 + - - +
85D LYS* 3.2 11.1 + - - +
86D GLU* 3.1 37.1 + - - +
87D LEU* 3.1 26.7 + - - +
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Residues in contact with LYS 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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6C ARG* 6.2 0.2 - - - +
55D ALA* 3.6 10.5 - - + +
57D ASP* 2.8 52.4 + - - +
58D VAL* 4.9 2.0 - - + -
59D ASP* 5.1 1.2 - - - +
83D SER* 1.3 70.3 + - - +
85D LYS* 1.3 63.7 + - + +
87D LEU* 4.2 0.4 - - - -
88D GLY 3.0 13.5 + - - -
96D ALA* 3.6 16.8 - - + -
97D ALA 2.8 44.5 + - - +
98D ALA* 4.4 1.6 - - - +
32E U 3.4 37.0 + - + +
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Residues in contact with LYS 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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57D ASP* 4.7 0.4 + - - +
83D SER* 3.2 7.8 + - - +
84D LYS* 1.3 82.8 - - + +
86D GLU* 1.3 61.7 + - - +
88D GLY* 3.4 2.3 + - - -
89D ALA* 3.2 27.0 + - - +
93D ILE 5.5 0.6 + - - -
94D GLU 3.3 26.3 + - - -
95D VAL* 4.1 2.4 - - - +
96D ALA* 3.9 24.0 - - + +
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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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18D GLU* 4.8 6.2 - - - +
21D LEU* 3.9 29.4 - - + +
82D PRO* 4.4 10.7 - - - +
83D SER* 3.1 27.7 + - - +
85D LYS* 1.3 75.8 - - - +
87D LEU* 1.3 62.0 - - - +
89D ALA* 3.5 6.4 + - + +
90D ALA* 3.2 22.5 + - - +
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Residues in contact with LEU 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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21D LEU* 3.8 17.4 - - + +
24D VAL* 4.3 9.9 - - + -
53D ILE* 3.7 43.3 - - + +
55D ALA* 4.0 3.8 - - + +
81D VAL* 3.8 17.3 - - + -
83D SER 3.1 17.7 + - - +
84D LYS 3.8 0.4 - - - +
86D GLU* 1.3 74.9 - - - +
88D GLY* 1.3 63.6 + - - +
90D ALA* 3.4 1.6 + - - +
91D ALA* 3.1 21.3 + - - +
97D ALA* 3.4 23.1 - - - +
98D ALA 4.0 9.9 - - - +
99D SER* 4.1 5.4 - - - -
100D VAL* 3.8 19.5 - - + +
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Residues in contact with GLY 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 LYS 3.0 12.0 + - - -
85D LYS 3.4 1.3 + - - -
86D GLU 3.3 0.4 - - - -
87D LEU* 1.3 74.7 - - - +
89D ALA* 1.3 63.1 + - - +
91D ALA* 3.0 10.6 + - - +
92D GLY 3.2 0.2 + - - -
93D ILE* 3.2 29.1 + - - +
95D VAL 3.4 17.9 - - - -
97D ALA* 3.7 19.4 - - - +
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Residues in contact with ALA 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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25D GLU* 4.4 1.1 - - - +
28D ARG* 3.6 7.6 + - - -
85D LYS* 3.2 18.3 + - - +
86D GLU* 3.8 10.3 - - + +
87D LEU 3.4 0.2 - - - -
88D GLY* 1.3 74.8 - - - +
90D ALA* 1.3 56.8 + - - +
92D GLY* 3.0 18.9 + - - -
93D ILE 3.7 11.6 + - - +
95D VAL 4.4 0.4 + - - -
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Residues in contact with ALA 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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21D LEU* 3.8 34.5 - - + +
24D VAL* 3.5 20.4 - - + +
25D GLU* 3.6 21.5 - - + +
28D ARG* 3.5 11.8 + - - -
86D GLU 3.2 14.3 + - - +
87D LEU 3.6 8.7 - - - +
88D GLY 3.2 0.4 - - - -
89D ALA* 1.3 76.1 - - - +
91D ALA* 1.3 59.3 + - - +
92D GLY 3.2 0.6 + - - -
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Residues in contact with ALA 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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24D VAL* 3.8 6.9 - - + +
28D ARG* 3.4 16.0 - - - +
33D ILE* 4.0 7.4 - - + +
35D LYS* 3.8 43.0 - - + +
87D LEU 3.1 12.1 + - - +
88D GLY* 3.0 12.8 + - - +
90D ALA* 1.3 74.9 - - - +
92D GLY* 1.3 59.8 + - - +
93D ILE* 3.8 4.2 + - + -
97D ALA* 5.0 0.7 - - + -
100D VAL* 4.1 12.6 - - + -
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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