Contacts of the helix formed by residues 81 - 92 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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75A LEU* 3.5 6.5 - - - -
79A GLY 3.8 1.2 + - - -
80A VAL* 1.3 73.8 - - - +
82A PRO* 1.3 77.8 - - - +
83A ARG 3.4 2.2 - - - -
84A LEU 3.1 3.5 + - - -
85A ALA* 2.9 21.1 + - - +
501A GOL 2.7 22.9 + - - -
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Residues in contact with PRO 82 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51A ILE* 3.7 31.2 - - + -
53A ARG* 4.5 12.6 - - - +
60A TYR* 3.3 31.0 - - + +
71A PHE* 3.7 5.1 - - + -
75A LEU* 3.4 14.5 - - + -
81A GLY* 1.3 80.5 - - - +
83A ARG* 1.3 61.9 + - + +
85A ALA* 3.4 2.9 + - - +
86A MET* 3.0 29.2 + - - +
501A GOL 3.3 17.7 - - - +
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Residues in contact with ARG 83 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60A TYR* 4.6 6.9 + - + +
82A PRO* 1.3 73.8 - - + +
84A LEU* 1.3 67.4 + - - +
86A MET* 2.9 9.8 + - - +
87A ALA* 2.9 22.8 + - - +
501A GOL 3.3 33.3 + - - +
158B LEU* 5.8 0.3 - - - +
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Residues in contact with LEU 84 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79A GLY 4.0 15.3 - - - +
80A VAL* 4.4 16.4 - - + -
81A GLY 3.1 4.8 + - - +
83A ARG* 1.3 78.5 - - - +
85A ALA* 1.3 56.9 + - - +
87A ALA* 3.2 6.7 + - + +
88A ALA* 2.9 29.1 + - - +
112A VAL* 4.3 3.8 - - + -
113A PRO 3.5 24.5 - - - +
114A GLY* 4.1 19.3 - - - +
115A ILE* 4.0 24.5 - - + -
123A MET* 6.3 0.7 - - - -
501A GOL 3.0 23.7 + - - +
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Residues in contact with ALA 85 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71A PHE* 3.6 23.1 - - + -
74A LEU* 3.8 20.8 - - + +
75A LEU* 3.8 13.5 - - + -
80A VAL* 4.3 6.9 - - + +
81A GLY 2.9 13.0 + - - +
82A PRO 3.4 9.6 - - - +
84A LEU* 1.3 78.0 - - - +
86A MET* 1.3 61.9 + - - +
88A ALA* 3.4 6.0 + - - +
89A LEU* 3.3 24.6 + - - +
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Residues in contact with MET 86 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15A ASP 5.5 0.2 - - - +
29A ASN* 4.1 4.0 - - + +
30A ALA* 3.3 47.8 - - - +
31A THR* 3.6 16.1 - - + +
60A TYR* 3.5 31.0 - - + -
62A PHE* 4.1 25.8 - - + -
71A PHE* 3.9 5.6 - - + -
82A PRO 3.0 16.6 + - - +
83A ARG* 2.9 10.8 + - - +
85A ALA* 1.3 77.2 - - - +
87A ALA* 1.3 51.9 + - - +
89A LEU* 3.1 7.1 + - - +
90A ALA* 2.7 36.2 + - + +
158B LEU* 5.0 5.2 - - + -
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Residues in contact with ALA 87 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83A ARG 2.9 11.5 + - - +
84A LEU* 3.5 15.0 - - + +
86A MET* 1.3 74.0 - - - +
88A ALA* 1.3 67.6 + - - +
90A ALA* 3.6 0.6 - - - +
91A VAL* 2.9 30.7 + - + +
112A VAL* 4.0 12.6 - - + -
113A PRO* 4.8 1.1 - - + +
158B LEU* 3.7 40.5 - - + +
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Residues in contact with ALA 88 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74A LEU* 4.5 7.6 - - + -
84A LEU 2.9 13.3 + - - +
85A ALA* 3.5 11.2 - - - +
86A MET 3.3 0.2 - - - -
87A ALA* 1.3 75.5 - - - +
89A LEU* 1.3 52.1 + - - +
91A VAL* 3.4 2.3 + - - +
92A HIS* 2.8 38.7 + - - +
97A LEU* 4.2 21.3 - - + +
112A VAL* 3.7 23.3 - - + +
115A ILE* 4.6 9.4 - - + -
123A MET* 5.3 4.3 - - + -
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Residues in contact with LEU 89 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31A THR* 3.9 13.4 - - + +
62A PHE* 3.9 29.4 - - + -
67A THR* 5.0 6.7 - - + -
70A LEU* 4.1 18.2 - - + -
71A PHE* 4.2 20.6 - - + +
74A LEU* 4.1 10.8 - - + -
85A ALA 3.3 13.2 + - - +
86A MET* 3.1 9.4 + - - +
88A ALA* 1.3 77.0 - - - +
90A ALA* 1.3 66.5 + - - +
91A VAL 3.1 1.6 - - - -
92A HIS 3.1 24.1 - - - +
93A ASP* 3.9 5.0 + - - +
94A ALA* 4.3 11.7 - - + +
97A LEU* 3.5 21.1 - - + -
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Residues in contact with ALA 90 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31A THR* 3.5 20.8 - - + +
32A PRO* 4.1 10.2 - - + +
33A ALA* 6.1 0.7 - - - +
86A MET 2.7 19.4 + - - +
87A ALA 3.1 4.9 + - - +
89A LEU* 1.3 74.8 - - - +
91A VAL* 1.3 61.8 + - + +
92A HIS 5.2 0.2 - - - -
93A ASP* 5.5 1.4 - - - +
158B LEU* 3.8 36.1 - - + -
189B LEU* 3.8 19.1 - - + +
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Residues in contact with VAL 91 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87A ALA* 2.9 20.1 + - + +
88A ALA 3.8 1.8 - - - +
90A ALA* 1.3 82.6 - - + +
92A HIS* 1.3 87.0 + - + +
93A ASP* 4.3 3.5 - - - +
111A ARG* 5.0 2.2 - - + -
112A VAL* 3.9 14.6 - - + +
113A PRO* 4.2 10.5 - - + -
158B LEU* 5.8 1.1 - - + -
160B PHE* 4.0 32.1 - - + -
189B LEU* 4.5 19.0 - - + +
190B SER* 5.9 0.5 - - - -
192B LEU 5.1 0.2 - - - +
193B GLY* 4.2 20.5 - - - +
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Residues in contact with HIS 92 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88A ALA 2.8 16.3 + - - +
89A LEU* 3.1 22.7 - - - +
91A VAL* 1.3 118.6 - - + +
93A ASP* 1.3 67.8 + - - +
94A ALA 3.6 0.2 + - - -
96A ALA* 4.5 5.8 - - + +
97A LEU* 3.7 31.2 - - + +
100A VAL* 3.9 16.5 - - + +
108A ALA* 3.3 47.2 + - + -
109A LEU* 4.2 4.7 - - + +
111A ARG* 4.7 1.2 - - - +
112A VAL* 4.3 4.3 - - + +
193B GLY* 4.6 14.1 + - - -
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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