Contacts of the helix formed by residues 81 - 97 (chain A) in PDB entry 2AFU
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 SER 81 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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76A GLU* 4.1 1.8 + - - -
77A ARG* 3.6 2.8 - - - -
78A TYR* 2.7 61.0 + - - -
79A PRO 3.2 1.6 + - - -
80A GLY* 1.3 82.0 - - - +
82A PRO* 1.3 76.4 - - - +
83A GLY 3.4 4.1 + - - -
84A SER* 3.1 21.3 + - - -
85A TYR* 3.4 9.7 + - - +
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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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78A TYR* 5.3 2.5 - - - +
80A GLY 4.7 0.4 - - - +
81A SER* 1.3 90.9 - - - +
83A GLY* 1.3 58.6 + - - +
85A TYR* 3.2 11.2 + - + +
86A ALA* 3.0 26.8 + - - +
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Residues in contact with GLY 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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75A ILE* 3.8 13.6 - - - +
76A GLU 3.3 21.4 + - - -
77A ARG* 3.7 7.2 - - - -
81A SER* 3.1 3.6 + - - -
82A PRO* 1.3 78.7 - - - +
84A SER* 1.3 54.0 + - - +
86A ALA* 3.0 3.6 + - - +
87A ALA* 2.7 37.4 + - - +
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Residues in contact with SER 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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77A ARG* 3.8 14.4 - - - +
78A TYR 3.4 20.4 - - - -
79A PRO* 4.3 1.4 - - - +
80A GLY 4.0 8.9 + - - -
81A SER* 3.1 18.6 + - - -
83A GLY* 1.3 74.8 - - - +
85A TYR* 1.3 63.0 + - - +
87A ALA* 3.4 3.7 + - - +
88A ARG* 3.0 45.7 + - - +
141A TYR* 3.7 11.8 + - - -
199A ASP* 4.3 7.4 + - - -
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Residues in contact with TYR 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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81A SER 3.4 6.7 + - - +
82A PRO* 3.2 12.7 + - + +
83A GLY 3.1 0.2 - - - -
84A SER* 1.3 81.2 - - - +
86A ALA* 1.3 64.8 + - + +
88A ARG* 3.4 26.9 + - - +
89A GLN* 3.0 67.1 + - + +
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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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72A PRO 6.0 0.4 - - - -
75A ILE* 4.1 15.5 - - + -
82A PRO 3.0 13.4 + - - +
83A GLY* 3.0 7.6 + - - +
85A TYR* 1.3 82.2 - - + +
87A ALA* 1.3 63.4 + - - +
89A GLN* 3.3 6.6 + - - +
90A HIS* 3.0 23.6 + - - +
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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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72A PRO 5.5 0.7 - - - -
73A LEU* 3.7 25.7 - - + +
75A ILE* 4.4 4.9 - - + +
77A ARG* 4.1 14.1 - - - -
83A GLY 2.7 20.0 + - - +
84A SER* 3.6 4.9 - - - +
86A ALA* 1.3 72.9 - - - +
88A ARG* 1.3 58.3 + - - +
90A HIS* 3.2 5.2 + - - +
91A ILE* 2.9 35.5 + - - +
141A TYR* 3.9 17.0 - - + -
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Residues in contact with ARG 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 SER* 3.0 39.6 + - - +
85A TYR* 3.6 36.6 - - - +
87A ALA* 1.3 79.0 - - - +
89A GLN* 1.3 60.9 + - - +
91A ILE* 3.6 1.6 + - - +
92A MET* 3.0 36.2 + - - +
106A ILE* 4.1 18.5 - - + +
121A SER* 3.7 30.7 + - - +
123A ILE* 3.2 34.0 - - + +
141A TYR* 2.9 27.4 + - - +
199A ASP* 4.5 2.0 + - - -
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Residues in contact with GLN 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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85A TYR* 3.0 62.6 + - + +
86A ALA* 3.7 6.5 - - - +
87A ALA 3.2 0.2 - - - -
88A ARG* 1.3 81.6 - - - +
90A HIS* 1.3 62.0 + - - +
92A MET* 3.8 16.5 - - - +
93A GLN* 2.8 51.8 + - - +
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Residues in contact with HIS 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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68A ASN 3.1 26.0 - - - -
69A ASP* 2.9 23.0 + - - -
72A PRO* 3.7 28.5 - - + +
73A LEU* 3.6 30.3 - - + -
86A ALA 3.0 13.7 + - - +
87A ALA* 3.4 9.4 - - - +
89A GLN* 1.3 76.9 - - - +
91A ILE* 1.3 57.9 + - - +
93A GLN* 3.2 13.1 + - - +
94A ARG* 2.8 53.5 + - + +
168A LEU* 4.0 6.5 - - + +
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Residues in contact with ILE 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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73A LEU* 4.6 11.7 - - + -
87A ALA 2.9 20.0 + - - +
88A ARG 3.9 3.4 - - - +
90A HIS* 1.3 76.6 - - + +
92A MET* 1.3 62.5 + - - +
94A ARG* 3.6 2.1 + - - +
95A ILE* 3.2 27.3 + - + +
123A ILE* 4.0 23.8 - - + -
141A TYR* 3.9 23.8 - - + -
164A CYS* 4.5 4.9 - - - -
168A LEU* 4.0 20.8 - - + +
197A PHE* 3.6 53.6 - - + -
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Residues in contact with MET 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 ARG* 3.0 20.1 + - - +
89A GLN* 3.8 21.1 - - - +
91A ILE* 1.3 74.8 - - - +
93A GLN* 1.3 66.5 + - + +
95A ILE* 3.1 3.6 + - - +
96A GLN* 2.9 37.6 + - - +
104A LEU* 4.0 37.9 - - + -
106A ILE* 3.3 42.0 - - + -
123A ILE* 4.5 11.0 - - + -
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Residues in contact with GLN 93 (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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89A GLN* 2.8 40.1 + - + +
90A HIS* 3.6 13.9 + - - +
92A MET* 1.3 75.6 - - + +
94A ARG* 1.3 64.4 + - + +
95A ILE 3.3 0.2 + - - -
96A GLN* 3.3 13.3 + - - +
97A ARG* 3.3 23.1 + - - +
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Residues in contact with ARG 94 (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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64A GLU 5.2 0.6 + - - -
68A ASN* 3.4 42.7 + - - +
69A ASP* 2.6 36.5 + - - +
90A HIS* 2.8 42.4 + - + +
91A ILE 3.9 4.3 - - - +
93A GLN* 1.3 78.1 - - + +
95A ILE* 1.3 57.6 + - - +
97A ARG* 3.2 58.3 + - - +
98A LEU* 3.6 12.5 - - - +
168A LEU* 4.1 12.1 - - + -
172A ARG* 4.5 13.5 - - - +
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Residues in contact with ILE 95 (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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91A ILE* 3.2 19.4 + - + +
92A MET 3.1 5.2 + - - +
94A ARG* 1.3 75.4 - - - +
96A GLN* 1.3 67.1 + - - +
97A ARG 3.2 0.2 - - - -
98A LEU* 3.1 28.9 + - + +
100A ALA 5.3 0.2 - - - +
102A TRP* 3.5 38.9 - - + +
104A LEU* 3.7 19.5 - - + -
125A SER* 3.4 29.4 - - - +
168A LEU* 3.9 13.9 - - + -
171A ALA* 5.4 2.7 - - + -
195A LEU* 4.5 8.5 - - + -
197A PHE* 4.2 20.0 - - + -
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Residues in contact with GLN 96 (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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92A MET* 2.9 31.8 + - - +
93A GLN* 3.3 11.9 + - - +
95A ILE* 1.3 77.3 - - - +
97A ARG* 1.3 60.7 + - - +
98A LEU 3.3 7.3 + - - +
102A TRP* 6.1 0.7 - - - -
104A LEU* 3.4 23.8 - - + +
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Residues in contact with ARG 97 (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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93A GLN 3.3 9.6 + - - +
94A ARG* 3.2 62.5 + - - +
96A GLN* 1.3 76.5 - - - +
98A LEU* 1.3 80.3 + - - +
99A GLN* 3.9 2.1 + - - +
172A ARG* 4.3 12.3 - - - +
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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