Contacts of the helix formed by residues 90 - 104 (chain A) in PDB entry 2AF0
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 90 (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* 4.2 6.9 + - - -
80A TRP* 3.5 28.0 + - - -
86A GLU 3.5 7.6 + - - -
87A LEU 3.3 8.7 + - - +
88A LEU 3.2 1.6 - - - +
89A ALA* 1.3 78.4 - - - +
91A LYS* 1.3 60.6 + - - +
92A TYR* 3.3 6.4 + - - +
93A GLY 3.1 14.2 + - - -
94A LEU* 2.9 30.2 + - - +
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Residues in contact with LYS 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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89A ALA 4.0 2.0 + - - -
90A SER* 1.3 73.3 + - - +
92A TYR* 1.3 81.4 + - + +
94A LEU* 3.5 8.8 + - - +
95A ALA* 3.0 27.5 + - - +
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Residues in contact with TYR 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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69A SER 3.0 19.9 + - - -
70A MET* 3.4 35.0 - - + -
71A LYS 4.4 4.3 - - - -
72A PRO* 3.8 19.0 - - + +
76A GLU* 3.5 31.0 - - - -
80A TRP* 3.6 16.1 - - + -
90A SER* 3.3 3.0 + - - +
91A LYS* 1.3 91.9 - - + +
93A GLY* 1.3 54.2 + - - +
95A ALA* 3.3 8.5 + - + +
96A ALA* 2.8 35.3 + - - +
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Residues in contact with GLY 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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80A TRP* 3.1 35.5 - - - -
87A LEU* 3.1 32.4 - - - +
90A SER* 3.1 4.6 + - - -
92A TYR* 1.3 74.6 - - - +
94A LEU* 1.3 57.2 + - - +
96A ALA* 3.7 0.5 - - - +
97A PHE* 3.0 24.9 + - - +
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Residues in contact with LEU 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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87A LEU* 3.4 3.5 + - - -
88A LEU* 4.3 25.1 - - + +
90A SER 2.9 18.4 + - - +
91A LYS* 3.6 8.7 - - - +
93A GLY* 1.3 74.1 - - - +
95A ALA* 1.3 59.8 + - - +
97A PHE* 3.5 3.3 + - + +
98A ARG* 2.9 43.0 + - + +
110A ILE* 4.2 31.0 - - + -
113A TRP* 5.6 0.9 - - + -
114A LEU* 3.9 32.8 - - + -
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Residues in contact with ALA 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 LYS 3.0 17.6 + - - +
92A TYR* 3.6 9.2 - - + +
94A LEU* 1.3 77.1 - - - +
96A ALA* 1.3 62.0 + - - +
98A ARG* 3.5 9.2 + - - +
99A ALA* 3.1 23.7 + - - +
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Residues in contact with ALA 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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72A PRO* 6.2 0.4 - - + -
80A TRP* 3.9 21.1 - - + -
92A TYR 2.8 20.4 + - - +
93A GLY 3.7 4.5 - - - +
95A ALA* 1.3 71.1 - - - +
97A PHE* 1.3 64.7 + - - +
99A ALA* 3.2 5.2 + - - +
100A PHE* 3.0 21.1 + - - +
189A PHE* 3.8 12.6 - - + -
194A PHE* 3.7 24.6 - - + -
198A LEU* 4.2 5.8 - - + -
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Residues in contact with PHE 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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84A PHE* 3.7 31.6 - + - -
87A LEU* 3.9 17.0 - - + -
88A LEU* 4.2 9.2 - - + -
93A GLY 3.0 19.3 + - - +
94A LEU* 3.7 4.9 - - + +
96A ALA* 1.3 71.8 - - - +
98A ARG* 1.3 66.0 + - - +
99A ALA 3.2 0.3 + - - -
100A PHE* 3.3 3.2 + + - +
101A LEU* 3.0 51.0 + - + +
110A ILE* 3.9 28.0 - - + -
181A MET* 4.0 4.0 - - + -
185A SER* 3.8 23.1 - - - -
186A TYR* 4.0 22.9 - - - -
189A PHE* 3.8 20.1 - + + -
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Residues in contact with ARG 98 (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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94A LEU* 2.9 29.2 + - + +
95A ALA* 3.8 8.1 - - - +
97A PHE* 1.3 76.2 - - - +
99A ALA* 1.3 57.6 + - - +
101A LEU* 3.5 2.4 + - - +
102A LYS* 2.9 30.1 + - - +
107A GLU* 4.4 5.0 - - + +
110A ILE* 3.8 30.0 - - + +
111A GLU* 3.5 38.4 + - - +
114A LEU* 4.0 26.7 - - - +
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Residues in contact with ALA 99 (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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95A ALA 3.1 17.9 + - - +
96A ALA* 3.2 6.3 + - - +
98A ARG* 1.3 72.4 - - - +
100A PHE* 1.3 65.8 + - - +
102A LYS* 3.8 8.1 - - - +
103A SER* 3.0 24.8 + - - -
194A PHE* 4.9 11.4 - - + -
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Residues in contact with PHE 100 (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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96A ALA 3.0 12.7 + - - +
97A PHE* 3.5 7.9 - + - +
99A ALA* 1.3 76.0 - - - +
101A LEU* 1.3 77.2 + - + +
103A SER* 2.6 28.8 + - - -
104A GLU* 3.3 38.8 + - + +
185A SER 3.6 9.9 - - - -
188A ARG* 3.7 19.5 - - + -
189A PHE* 3.6 47.6 - + + -
192A SER* 3.9 29.2 - - - -
194A PHE* 4.9 11.9 - + + -
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Residues in contact with LEU 101 (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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97A PHE* 3.0 39.2 + - + +
98A ARG* 3.8 3.6 - - - +
100A PHE* 1.3 87.0 - - + +
102A LYS* 1.3 60.2 + - - +
104A GLU* 3.2 5.7 + - - +
105A PHE 3.0 7.8 + - - -
106A CYS* 2.9 48.3 + - - +
107A GLU* 3.9 14.1 - - - +
109A ASN* 5.7 0.2 - - + -
110A ILE* 3.5 37.2 - - + +
181A MET* 4.8 3.8 - - + -
185A SER* 3.6 30.1 - - - +
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Residues in contact with LYS 102 (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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98A ARG 2.9 19.8 + - - +
99A ALA* 3.8 8.1 - - - +
101A LEU* 1.3 77.1 - - - +
103A SER* 1.3 58.8 + - - +
105A PHE* 3.0 25.1 + - - -
107A GLU* 3.9 35.3 - - + +
111A GLU* 5.7 2.9 - - - -
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Residues in contact with SER 103 (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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99A ALA 3.0 13.1 + - - -
100A PHE* 2.6 26.1 + - - -
102A LYS* 1.3 76.7 - - - +
104A GLU* 1.3 62.8 + - - +
105A PHE* 3.4 19.7 - - - -
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Residues in contact with GLU 104 (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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100A PHE* 3.3 33.9 + - + +
101A LEU* 3.2 6.5 + - - +
102A LYS 3.1 0.4 - - - -
103A SER* 1.3 84.6 + - - +
105A PHE* 1.3 76.3 + - - +
106A CYS* 3.1 16.0 + - - +
188A ARG* 3.1 44.8 + - - -
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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