Contacts of the helix formed by residues 82 - 93 (chain D) in PDB entry 3O9Z
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 LEU 82 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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53A GLU* 3.8 27.1 - - + +
55A GLU* 3.8 26.9 - - + +
56A ALA* 5.6 0.4 - - + -
78D SER* 3.5 11.7 - - - +
79D PRO* 3.0 19.3 + - + +
81D HIS* 1.3 93.6 - - + +
83D HIS* 1.3 64.6 + - - +
84D TYR 3.4 0.9 - - - -
85D PRO* 3.3 15.1 - - + +
86D GLN* 3.0 27.1 + - - +
311D NAD 3.2 47.6 - - + +
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Residues in contact with HIS 83 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76D ILE* 3.6 12.9 - - + +
78D SER* 2.7 33.6 + - - -
79D PRO 3.3 13.3 + - - -
80D ASN* 3.1 18.0 + - - +
82D LEU* 1.3 78.0 - - - +
84D TYR* 1.3 59.9 + - - +
86D GLN* 3.7 0.9 - - - +
87D ILE* 2.8 36.0 + - + +
99D SER* 3.3 8.9 + - - +
100D GLU* 3.1 28.4 + - + +
101D LYS 3.4 8.3 - - - -
102D PRO 2.7 19.3 + - - +
103D LEU 3.1 16.4 - - - +
104D VAL* 4.7 0.4 - - - -
311D NAD 2.8 18.9 + - - -
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Residues in contact with TYR 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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59A ALA* 4.9 6.1 - - + -
63A ASP* 4.5 4.7 + - - -
80D ASN 4.6 1.2 + - - -
81D HIS 4.4 1.9 + - - +
83D HIS* 1.3 80.3 - - - +
85D PRO* 1.3 68.8 - - + +
87D ILE* 3.2 2.9 + - - +
88D ARG* 2.8 68.5 + - + +
104D VAL* 3.6 20.8 - - + +
105D LEU 5.5 0.2 - - - +
109D GLU* 3.6 62.8 - - + +
112D ARG* 3.1 20.0 - - + +
113D LEU* 3.7 25.1 - - + -
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Residues in contact with PRO 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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55A GLU* 3.5 36.3 - - + +
56A ALA* 3.8 13.2 - - + +
59A ALA* 4.4 5.2 - - + -
81D HIS 3.3 18.8 - - - +
82D LEU* 3.3 28.5 - - + +
84D TYR* 1.3 102.9 - - + +
86D GLN* 1.3 54.4 + - - +
88D ARG* 3.4 12.1 - - + +
89D MET* 3.1 23.6 + - - +
92D ARG* 4.8 2.4 + - - -
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Residues in contact with GLN 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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55A GLU* 2.9 27.7 + - + +
7D THR* 2.7 32.7 + - + +
32D LEU* 3.9 2.2 - - + +
74D LEU* 3.4 13.1 - - + +
76D ILE* 3.6 16.1 - - + +
78D SER* 2.8 19.2 + - - -
82D LEU* 3.0 19.5 + - + +
83D HIS 3.9 1.8 - - - +
85D PRO* 1.3 75.1 - - - +
87D ILE* 1.3 59.1 + - - +
89D MET* 3.1 11.5 + - + +
90D ALA 3.0 22.2 + - - -
311D NAD 2.8 39.6 + - - -
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Residues in contact with ILE 87 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76D ILE* 3.6 17.7 - - + -
83D HIS 2.8 27.7 + - - +
84D TYR 3.5 3.8 - - - +
86D GLN* 1.3 68.1 - - - +
88D ARG* 1.3 67.5 + - - +
90D ALA* 3.1 7.1 + - - +
91D LEU* 3.0 23.8 + - + +
97D ALA* 4.1 11.4 - - + -
99D SER* 4.2 4.7 - - - -
103D LEU* 3.6 42.0 - - + +
104D VAL* 4.1 10.5 - - + -
113D LEU* 3.6 17.3 - - + -
124D VAL* 3.6 34.3 - - + -
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Residues in contact with ARG 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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59A ALA* 3.3 21.1 + - + +
62A GLU* 2.7 34.0 + - - +
63A ASP* 2.8 33.7 + - - -
84D TYR* 2.8 73.2 + - + +
85D PRO* 3.4 12.3 - - + +
87D ILE* 1.3 76.3 - - - +
89D MET* 1.3 63.8 + - - +
91D LEU* 3.4 6.5 + - - +
92D ARG* 3.0 37.1 + - - +
112D ARG* 3.7 6.3 - - - +
113D LEU* 4.0 4.5 - - + -
116D LEU* 3.4 31.9 - - - +
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Residues in contact with MET 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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55A GLU* 4.1 25.4 - - + -
58A GLU* 4.8 1.8 - - - +
32D LEU* 5.5 1.1 - - + -
54D PRO* 4.3 8.7 - - + +
57D PHE* 3.9 31.6 - - + -
58D GLU* 3.6 40.2 - - + +
74D LEU* 4.7 6.3 - - + -
85D PRO 3.1 12.2 + - - +
86D GLN* 3.3 14.1 - - + +
87D ILE 3.1 0.2 - - - -
88D ARG* 1.3 76.2 - - - +
90D ALA* 1.3 62.7 + - - +
92D ARG* 3.2 18.5 + - - +
93D LEU* 2.9 44.3 + - + +
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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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74D LEU* 3.8 28.7 - - + +
86D GLN 3.0 12.2 + - - +
87D ILE 3.3 8.5 - - - +
89D MET* 1.3 75.8 - - - +
91D LEU* 1.3 62.4 + - + +
93D LEU* 3.1 13.4 + - - +
94D GLY 3.2 0.2 + - - -
95D ALA* 2.9 31.9 + - + +
96D ASN 4.0 7.4 - - - +
97D ALA* 3.9 18.8 - - + -
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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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87D ILE* 3.0 21.0 + - + +
88D ARG* 3.8 4.9 - - - +
90D ALA* 1.3 76.9 - - + +
92D ARG* 1.3 64.1 + - - +
94D GLY* 3.0 13.9 + - - -
95D ALA 3.8 15.0 - - - +
96D ASN* 5.2 0.2 - - - -
97D ALA 5.4 0.9 - - - +
113D LEU* 4.2 20.6 - - + +
116D LEU* 3.7 36.8 - - + -
117D GLU* 4.3 2.2 - - + +
120D THR* 3.7 29.1 - - + +
122D ARG* 3.9 24.7 - - + +
123D ARG 4.5 2.5 - - - +
124D VAL* 4.2 20.9 - - + -
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Residues in contact with ARG 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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55A GLU* 5.2 1.4 + - - +
58A GLU* 3.1 30.3 + - - +
59A ALA* 4.2 10.3 - - - +
62A GLU* 2.9 45.2 + - - +
92A ARG* 3.6 22.9 - - - +
93A LEU* 5.9 0.2 - - - +
58D GLU* 2.8 36.2 + - - +
62D GLU* 6.0 0.2 - - - +
65D ARG* 3.0 19.8 + - - -
85D PRO 4.8 2.2 + - - -
88D ARG* 3.0 28.6 + - - +
89D MET* 3.2 30.6 + - - +
91D LEU* 1.3 75.7 - - - +
93D LEU* 1.3 59.0 + - + +
94D GLY 3.2 1.1 + - - -
120D THR* 5.4 2.0 - - - -
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Residues in contact with LEU 93 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92A ARG* 6.1 0.2 - - - +
58D GLU* 3.8 13.7 - - + +
61D LEU* 3.7 34.5 - - + +
62D GLU* 3.5 45.5 - - + +
65D ARG* 3.5 30.2 - - + +
70D GLY* 5.8 1.6 - - - -
71D VAL* 5.1 7.9 - - + +
74D LEU* 5.5 2.5 - - + -
89D MET* 2.9 39.2 + - + +
90D ALA* 3.1 9.4 + - - +
92D ARG* 1.3 79.0 - - + +
94D GLY* 1.3 60.4 + - - +
95D ALA* 3.5 6.4 + - + +
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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