Contacts of the helix formed by residues 78 - 91 (chain D) in PDB entry 2PGW
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 78 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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74D HIS* 5.8 0.7 - - + +
75D SER* 3.1 25.0 + - - +
77D HIS* 1.3 81.8 - - - +
79D VAL* 1.3 63.9 + - - +
80D ALA 3.3 2.7 - - - -
81D PRO* 3.1 12.5 - - + +
82D LEU* 3.0 35.7 + - + +
126H HIS* 5.8 0.2 - - - -
127H GLN* 3.1 26.2 + - - +
130H GLY 3.4 5.2 - - - -
131H GLY* 3.8 10.8 - - - -
132H ALA* 4.3 4.7 + - - +
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Residues in contact with VAL 79 (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 PRO 3.8 2.7 + - - +
77D HIS 3.4 0.2 - - - -
78D ASP* 1.3 75.6 - - - +
80D ALA* 1.3 69.6 + - - +
82D LEU* 3.7 1.9 - - - +
83D ILE* 3.0 39.1 + - + +
110D ASP* 3.3 22.4 - - - +
113D MSE 3.7 44.7 - - + +
114D TRP* 3.8 22.4 - - + +
117D GLN* 3.8 20.6 - - - +
279D GLN* 4.3 1.8 - - - +
130H GLY* 3.8 8.5 - - - +
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Residues in contact with ALA 80 (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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79D VAL* 1.3 76.4 - - - +
81D PRO* 1.3 68.4 - - + +
83D ILE* 3.4 5.1 + - - +
84D ALA* 3.1 21.1 + - - +
279D GLN* 3.3 24.0 - - - +
129H LEU 5.1 0.7 - - - +
130H GLY* 2.9 20.8 + - - +
133H HIS* 3.8 18.4 - - + +
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Residues in contact with PRO 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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78D ASP* 3.1 26.9 - - + +
80D ALA* 1.3 84.4 - - + +
82D LEU* 1.3 63.8 + - + +
84D ALA* 3.2 4.0 + - + +
85D ARG* 2.9 24.6 + - - +
130H GLY 3.1 17.5 - - - +
131H GLY* 3.9 7.2 - - - -
132H ALA 3.2 27.8 - - - +
133H HIS* 3.7 26.0 - - + +
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Residues in contact with LEU 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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70D HIS* 4.9 2.0 - - + +
71D LEU* 4.0 20.6 - - + -
74D HIS* 3.7 42.6 - - + +
75D SER 3.5 22.7 - - - +
78D ASP* 3.0 30.9 + - + +
79D VAL* 3.7 3.6 - - - +
81D PRO* 1.3 76.8 - - + +
83D ILE* 1.3 64.7 + - - +
85D ARG* 3.3 11.4 + - - +
86D ILE* 3.0 32.1 + - + +
113D MSE 3.9 13.2 - - + -
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Residues in contact with ILE 83 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71D LEU* 5.6 1.8 - - + -
79D VAL* 3.0 40.7 + - + +
80D ALA* 3.8 5.4 - - - +
82D LEU* 1.3 76.6 - - + +
84D ALA* 1.3 58.8 + - - +
86D ILE* 3.3 5.4 + - + +
87D PHE* 2.9 29.6 + - + +
106D PHE* 3.5 46.1 - - + +
109D ILE* 4.2 18.2 - - + -
110D ASP* 4.0 22.0 - - + +
276D GLY 5.3 1.3 - - - +
280D PRO* 6.5 0.4 - - + -
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Residues in contact with ALA 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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80D ALA 3.1 14.7 + - - +
81D PRO* 3.5 11.4 - - + +
82D LEU 3.2 0.2 - - - -
83D ILE* 1.3 78.6 - - - +
85D ARG* 1.3 61.4 + - - +
87D PHE* 3.4 9.0 + - - +
88D HIS* 3.0 23.7 + - - +
133H HIS* 4.9 9.2 - - + +
318H PRO* 6.4 0.4 - - + -
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Residues in contact with ARG 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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81D PRO 2.9 15.8 + - - +
82D LEU* 3.3 11.0 + - + +
84D ALA* 1.3 72.5 - - - +
86D ILE* 1.3 64.1 + - + +
88D HIS* 3.2 1.5 + - - -
89D GLN* 2.8 36.1 + - - +
26E TYR* 3.2 43.5 + - + +
135H LYS* 5.1 10.7 - - - +
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Residues in contact with ILE 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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67D LEU* 3.6 45.8 - - + +
70D HIS* 3.5 35.9 - - + +
71D LEU* 3.8 23.1 - - + -
82D LEU* 3.0 26.2 + - + +
83D ILE* 3.7 7.4 - - + +
85D ARG* 1.3 78.6 - - + +
87D PHE* 1.3 58.0 + - - +
89D GLN* 4.4 5.2 - - - -
90D GLU* 2.9 36.1 + - + +
91D TYR* 4.4 0.2 - - - -
106D PHE* 3.7 10.8 - - + -
109D ILE* 6.2 0.9 - - + -
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Residues in contact with PHE 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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83D ILE* 2.9 19.1 + - + +
84D ALA* 3.6 7.9 - - - +
86D ILE* 1.3 77.3 - - - +
88D HIS* 1.3 57.5 + - - +
91D TYR* 3.0 61.7 + + + +
92D LEU* 3.2 28.8 + - + +
96D ALA 4.9 0.2 - - - -
98D ILE 4.4 2.9 - - - -
99D MSE 3.9 37.0 - - + -
102D ALA* 3.5 25.8 - - + -
106D PHE* 3.7 15.5 - + + -
228E TRP* 3.9 21.8 - + - -
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Residues in contact with HIS 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 ALA 3.0 17.7 + - - +
85D ARG* 3.7 0.7 - - - +
87D PHE* 1.3 76.9 - - - +
89D GLN* 1.3 57.6 + - - +
92D LEU* 3.9 31.0 - - + +
93D GLY* 2.8 33.7 + - - -
25E SER* 3.5 30.7 - - - -
26E TYR* 3.0 25.0 - - - +
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Residues in contact with GLN 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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70D HIS* 3.6 32.0 + - - -
85D ARG* 2.8 25.9 + - - +
86D ILE* 3.9 4.3 - - - +
88D HIS* 1.3 79.3 - - - +
90D GLU* 1.3 65.4 + - + +
93D GLY* 4.5 0.2 - - - -
94D HIS* 3.2 24.1 + - - -
24E TRP* 3.4 12.1 - - + -
26E TYR* 3.5 45.8 - - + +
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Residues in contact with GLU 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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66D ARG* 2.9 47.7 + - - +
67D LEU* 4.1 16.8 - - + -
70D HIS* 2.8 37.7 + - + +
86D ILE* 2.9 22.0 + - + +
89D GLN* 1.3 84.3 + - + +
91D TYR* 1.3 68.7 + - + +
94D HIS* 3.7 11.8 + - - -
54E ALA* 3.6 10.0 - - - +
55E PRO* 3.6 25.1 - - + +
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Residues in contact with TYR 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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63D ILE* 3.8 6.6 - - - +
67D LEU* 3.6 34.1 - - + +
87D PHE* 3.0 39.4 + + + +
89D GLN 3.5 0.2 - - - -
90D GLU* 1.3 83.4 - - + +
92D LEU* 1.3 66.8 + - - +
93D GLY 3.2 1.3 - - - -
94D HIS* 2.9 13.0 + - - -
96D ALA* 3.0 34.3 + - + +
98D ILE* 3.6 36.6 - - + -
101D ALA* 4.7 1.4 + - + -
102D ALA* 3.8 30.8 - - + -
105D ILE* 4.1 4.3 - - - +
106D PHE* 4.2 4.9 - + - -
55E PRO* 3.6 34.8 - - + +
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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