Contacts of the helix formed by residues 77 - 91 (chain A) in PDB entry 2O5F
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 THR 77 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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35A ARG* 5.5 2.7 - - - +
72A VAL* 4.2 2.0 - - - -
75A GLY 4.1 0.4 + - - -
76A GLU* 1.3 79.8 - - - +
78A TYR* 1.3 72.0 + - - +
79A GLU* 3.6 10.7 + - + +
80A GLU* 3.1 45.4 + - + +
81A ALA* 3.1 19.6 + - - +
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Residues in contact with TYR 78 (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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16A ASP* 2.9 25.1 + - - -
35A ARG* 2.8 52.3 - - + +
36A VAL 3.7 15.9 - - - -
37A VAL* 3.4 28.0 - - + +
72A VAL* 4.1 6.0 - - + +
77A THR* 1.3 79.5 + - - +
79A GLU* 1.3 63.7 + - - +
81A ALA* 3.2 2.6 + - - -
82A PHE* 3.0 20.1 + - - +
115A PHE* 3.9 7.4 - - - +
116A MET* 4.0 6.3 + - - -
117A CYS* 3.7 22.4 - - + -
119A TYR* 3.2 16.6 - - - +
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Residues in contact with GLU 79 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77A THR* 3.3 10.3 + - + +
78A TYR* 1.3 77.6 - - - +
80A GLU* 1.3 58.6 + - + +
82A PHE* 3.2 6.0 + - + +
83A ARG* 2.9 57.0 + - - +
94A ILE* 4.4 2.2 - - + +
99A TRP* 3.6 35.3 - - + -
119A TYR* 3.3 10.4 + - + +
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Residues in contact with GLU 80 (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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75A GLY 4.3 3.3 - - - +
76A GLU* 3.5 24.4 - - + +
77A THR* 3.1 35.6 + - + +
79A GLU* 1.3 78.0 - - + +
81A ALA* 1.3 63.0 + - - +
83A ARG* 3.4 17.7 + - - +
84A ARG* 3.0 23.9 + - - +
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Residues in contact with ALA 81 (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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37A VAL* 3.9 11.0 - - + -
72A VAL* 3.9 23.1 - - + -
76A GLU* 3.2 27.7 - - - +
77A THR 3.1 10.7 + - - +
78A TYR 3.6 8.1 - - - +
80A GLU* 1.3 76.9 - - - +
82A PHE* 1.3 57.0 + - - +
84A ARG* 3.3 10.2 + - - +
85A GLU* 2.9 35.3 + - - +
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Residues in contact with PHE 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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37A VAL* 4.1 10.9 - - + +
38A ASN 5.8 0.2 - - - -
39A ALA* 3.5 25.6 - - + -
68A VAL* 4.7 9.9 - - + -
78A TYR 3.0 12.0 + - - +
79A GLU* 3.2 9.2 + - - +
81A ALA* 1.3 76.9 - - - +
83A ARG* 1.3 62.7 + - - +
84A ARG 3.2 0.2 + - - -
85A GLU* 3.9 1.6 - - - +
86A ALA* 2.9 29.5 + - + +
94A ILE* 3.8 34.5 - - + -
99A TRP* 3.7 33.0 - + + -
119A TYR* 3.7 46.4 - + + -
121A LEU* 3.8 17.9 - - + -
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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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79A GLU* 2.9 45.0 + - - +
80A GLU* 3.8 17.9 - - - +
82A PHE* 1.3 75.5 - - - +
84A ARG* 1.3 62.8 + - - +
86A ALA* 3.7 1.6 + - - +
87A ARG* 3.2 45.3 + - - +
92A VAL 4.6 1.4 - - - +
93A GLU* 6.0 1.6 - - - -
94A ILE* 3.6 31.7 - - + +
95A ASP* 2.8 42.4 + - - +
99A TRP* 5.0 0.4 - - - -
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Residues in contact with ARG 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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71A ALA 3.0 24.4 + - - -
73A GLN* 3.7 29.6 + - - +
76A GLU* 2.9 40.5 + - - +
80A GLU 3.0 16.0 + - - +
81A ALA* 3.6 11.3 + - - +
82A PHE 3.2 0.2 - - - -
83A ARG* 1.3 77.6 - - - +
85A GLU* 1.3 88.0 + - - +
87A ARG* 3.1 14.3 - - + +
88A GLU* 3.0 38.8 + - + +
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Residues in contact with GLU 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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37A VAL* 4.4 6.7 - - + -
68A VAL* 3.5 17.0 - - + -
69A GLY 3.7 2.2 - - - +
70A GLY* 3.3 35.5 - - - +
71A ALA 4.0 2.4 + - - +
81A ALA 2.9 25.0 + - - +
82A PHE* 4.0 2.0 - - - +
84A ARG* 1.3 91.2 + - - +
86A ALA* 1.3 60.4 + - - +
88A GLU* 2.5 28.6 - - - +
89A GLU* 2.9 54.3 + - - +
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Residues in contact with ALA 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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68A VAL* 3.4 21.7 - - + +
82A PHE* 2.9 23.3 + - + +
83A ARG 3.9 1.6 - - - +
85A GLU* 1.3 76.8 - - - +
87A ARG* 1.3 58.0 + - - +
90A LEU* 3.0 25.6 + - - +
91A ASN 3.1 5.5 + - - -
92A VAL* 3.2 19.3 + - + +
94A ILE* 3.7 25.4 - - + -
121A LEU* 5.4 1.8 - - + -
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Residues in contact with ARG 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* 3.2 37.0 + - - +
84A ARG* 3.1 21.5 - - + +
86A ALA* 1.3 81.4 - - - +
88A GLU* 1.3 59.7 + - + +
91A ASN* 3.1 30.6 + - - -
92A VAL 3.4 19.7 + - - +
93A GLU* 3.1 33.9 + - - +
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Residues in contact with GLU 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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84A ARG* 3.0 35.2 + - + +
85A GLU* 2.5 39.0 - - - +
87A ARG* 1.3 80.3 - - + +
89A GLU* 1.3 65.3 + - + +
91A ASN* 5.3 1.3 + - - +
130A ASN* 3.3 28.8 + - - +
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Residues in contact with GLU 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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53A ARG* 3.6 26.9 + - - +
68A VAL* 3.3 15.1 - - - +
69A GLY 3.0 39.0 + - - +
85A GLU* 2.9 32.0 + - - +
88A GLU* 1.3 85.6 - - + +
90A LEU* 1.3 66.1 + - + +
91A ASN 3.6 0.2 - - - -
129A PHE* 3.6 4.2 - - - +
130A ASN* 2.9 27.6 + - - +
133A ASP* 4.1 17.4 - - + +
134A ILE* 3.9 6.4 - - + +
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Residues in contact with LEU 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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41A LEU* 4.9 6.5 - - + -
49A TRP* 3.5 31.0 - - + -
53A ARG* 3.8 6.1 - - - +
67A SER* 3.6 24.9 - - - +
68A VAL* 3.3 30.1 - - + -
86A ALA 3.0 11.6 + - - +
89A GLU* 1.3 84.4 - - + +
91A ASN* 1.3 72.9 + - - +
92A VAL* 3.2 21.4 + - + +
121A LEU* 5.2 4.5 - - + -
127A PRO* 4.2 18.2 - - + -
128A ILE 3.4 18.2 + - - +
129A PHE* 4.1 7.6 - - + +
134A ILE* 4.0 2.2 - - + -
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Residues in contact with ASN 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 ARG* 3.1 26.3 + - - +
88A GLU* 5.4 0.8 + - - +
90A LEU* 1.3 80.1 - - - +
92A VAL* 1.3 61.0 + - - +
93A GLU* 4.3 4.5 + - - +
128A ILE* 2.9 27.8 + - + +
129A PHE 4.0 10.4 - - - +
130A ASN* 4.0 9.4 + - - +
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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