Contacts of the helix formed by residues 81 - 92 (chain D) in PDB entry 2H5X
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 81 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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75D LEU* 3.4 6.3 - - - -
79D GLY 3.7 3.4 + - - -
80D VAL* 1.3 74.4 - - - +
82D PRO* 1.3 76.2 - - - +
85D ALA* 3.0 22.7 + - - +
504D GOL 3.3 26.2 + - - -
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Residues in contact with PRO 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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51D ILE* 4.3 28.3 - - + -
53D ARG* 4.7 12.1 - - - +
60D TYR* 3.1 33.7 - - + +
71D PHE* 4.2 4.0 - - + -
75D LEU* 3.7 19.7 - - + -
81D GLY* 1.3 81.6 - - - +
83D ARG* 1.3 61.8 + - - +
85D ALA* 3.1 2.5 + - + +
86D MET* 2.9 29.5 + - - +
504D GOL 3.4 17.3 - - - +
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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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158A LEU* 5.6 0.9 - - - +
60D TYR* 4.7 4.7 + - - +
82D PRO* 1.3 76.0 - - - +
84D LEU* 1.3 59.5 + - - +
86D MET* 3.3 7.9 + - - +
87D ALA* 3.0 25.7 + - - +
504D GOL 3.2 42.8 + - - +
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Residues in contact with LEU 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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79D GLY 4.5 6.5 - - - +
80D VAL* 4.1 30.1 - - + -
81D GLY 4.0 2.2 - - - +
83D ARG* 1.3 77.8 - - - +
85D ALA* 1.3 60.1 + - - +
87D ALA* 4.1 5.2 - - + -
88D ALA* 2.8 29.9 + - + +
112D VAL* 4.3 3.8 - - + -
113D PRO 3.4 26.0 - - - +
114D GLY* 4.0 17.0 - - - +
115D ILE* 4.1 26.0 - - + -
123D MET* 5.1 1.3 - - + -
504D GOL 3.0 17.2 + - - +
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Residues in contact with ALA 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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71D PHE* 3.4 24.7 - - + -
74D LEU* 3.7 23.2 - - + +
75D LEU* 3.9 11.9 - - + -
80D VAL* 4.2 7.2 - - + +
81D GLY 3.0 19.5 + - - +
82D PRO 3.4 4.9 - - - +
84D LEU* 1.3 76.5 - - - +
86D MET* 1.3 62.3 + - - +
88D ALA* 3.5 4.8 + - - +
89D LEU* 3.2 26.0 + - - +
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Residues in contact with MET 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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158A LEU* 5.0 4.0 - - + -
15D ASP 5.6 0.2 - - - +
29D ASN* 4.1 7.0 - - + +
30D ALA* 3.4 46.2 - - - +
31D THR* 3.5 16.5 - - + +
60D TYR* 3.6 25.4 - - + -
62D PHE* 4.0 19.7 - - + -
71D PHE* 3.8 15.9 - - + -
82D PRO 2.9 15.4 + - - +
83D ARG* 3.4 10.3 - - - +
85D ALA* 1.3 75.8 - - - +
87D ALA* 1.3 59.7 + - - +
89D LEU* 3.2 5.6 + - - +
90D ALA* 2.8 28.3 + - - +
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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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158A LEU* 3.7 43.5 - - + +
83D ARG 3.0 16.5 + - - +
84D LEU* 3.7 11.9 - - + +
86D MET* 1.3 72.2 - - - +
88D ALA* 1.3 69.9 + - - +
90D ALA* 2.8 13.4 + - - +
91D VAL* 2.9 17.0 + - + +
112D VAL* 4.2 12.8 - - + -
113D PRO* 4.7 1.3 - - + +
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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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74D LEU* 4.7 5.6 - - + -
80D VAL* 6.5 0.2 - - + -
84D LEU 2.8 17.9 + - - +
85D ALA* 3.6 8.1 - - - +
87D ALA* 1.3 76.9 - - - +
89D LEU* 1.3 58.5 + - - +
91D VAL* 3.3 2.8 + - - +
92D HIS* 2.8 31.0 + - - +
97D LEU* 4.4 17.7 - - + -
109D LEU* 5.8 0.9 - - + -
112D VAL* 3.7 23.4 - - + +
115D ILE* 4.3 13.2 - - + -
123D MET* 5.9 1.8 - - - -
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Residues in contact with LEU 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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31D THR* 4.0 14.6 + - + +
33D ALA* 6.0 1.4 - - - +
62D PHE* 3.6 33.7 - - + -
67D THR* 4.6 8.5 - - + +
70D LEU* 4.0 16.4 - - + -
71D PHE* 4.3 20.2 - - + +
74D LEU* 4.3 2.5 - - + -
85D ALA 3.2 14.9 + - - +
86D MET* 3.5 9.6 - - - +
87D ALA 3.1 0.4 - - - -
88D ALA* 1.3 78.0 - - - +
90D ALA* 1.3 62.5 + - - +
92D HIS 2.7 25.3 - - - +
93D ASP* 3.8 5.0 + - - +
94D ALA* 4.1 13.2 - - + +
97D LEU* 3.4 24.5 - - + -
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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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158A LEU* 4.1 24.9 - - + -
189A LEU* 3.9 19.5 - - + +
31D THR* 4.2 11.4 - - - -
32D PRO* 4.0 21.7 - - + +
33D ALA* 6.1 1.3 - - - +
86D MET 2.8 12.7 + - - +
87D ALA* 2.8 13.4 + - - +
89D LEU* 1.3 74.2 - - - +
91D VAL* 1.3 61.8 + - + +
92D HIS* 4.8 0.3 - - - -
93D ASP 5.3 0.3 + - - -
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Residues in contact with VAL 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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158A LEU* 6.0 1.8 - - + -
160A PHE* 4.0 29.8 - - + -
189A LEU* 4.4 11.6 - - + +
193A GLY* 4.0 25.4 - - - -
87D ALA* 2.9 17.4 + - + +
90D ALA* 1.3 81.0 - - + +
92D HIS* 1.3 78.1 + - + +
93D ASP 4.3 0.7 - - - -
111D ARG* 4.5 9.0 - - + +
112D VAL* 3.8 21.1 - - + +
113D PRO* 4.1 13.7 - - + -
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Residues in contact with HIS 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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193A GLY* 4.4 14.8 - - - -
88D ALA 2.8 9.4 + - - +
89D LEU* 2.7 31.4 - - - +
91D VAL* 1.3 103.0 + - + +
93D ASP* 1.3 63.5 + - - +
96D ALA* 4.7 6.6 - - + +
97D LEU* 3.8 25.3 - - + +
100D VAL* 4.5 15.3 - - + +
108D ALA* 3.1 40.0 + - + +
109D LEU* 4.6 10.3 - - + -
111D ARG* 4.9 2.9 - - - -
112D VAL* 4.0 20.0 - - + -
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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