Contacts of the helix formed by residues 89 - 102 (chain A) in PDB entry 2A7P
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 LYS 89 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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84A GLY* 4.9 4.3 - - - -
87A TRP 3.3 0.6 + - - -
88A PRO* 1.3 76.5 - - + +
90A GLY* 1.3 64.4 + - - +
91A ASP 3.2 3.1 - - - -
92A LEU* 3.1 14.2 + - + -
93A ALA* 3.0 19.4 + - - +
113A MET* 4.3 20.0 - - + -
121A GLN* 5.8 1.6 - - - +
890A MES 3.1 53.1 + - - +
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Residues in contact with GLY 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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83A ASN* 3.8 18.6 - - - -
84A GLY* 4.2 4.4 - - - -
87A TRP 2.9 17.4 + - - -
88A PRO 3.8 1.8 - - - -
89A LYS* 1.3 77.6 - - - +
91A ASP* 1.3 63.5 + - - +
93A ALA* 3.2 2.5 + - - +
94A LEU* 3.0 28.1 + - - +
314A LEU* 3.9 17.7 - - - -
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Residues in contact with ASP 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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80A THR 4.5 1.0 - - - +
83A ASN* 2.8 36.4 + - - +
84A GLY 4.7 0.4 + - - +
89A LYS 3.2 1.2 - - - -
90A GLY* 1.3 74.5 - - - +
92A LEU* 1.3 62.4 + - - +
94A LEU* 3.3 4.5 + - - +
95A ALA* 3.1 23.2 + - - +
105A PHE* 3.7 7.5 - - + -
107A LEU* 4.0 13.7 - - + +
108A SER 5.5 0.5 + - - -
111A SER* 3.8 18.6 - - - -
112A ASN* 2.8 35.5 + - - +
113A MET* 3.3 23.7 + - + +
118A LEU* 4.5 3.1 - - + -
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Residues in contact with LEU 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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89A LYS* 3.1 12.3 + - + +
91A ASP* 1.3 75.6 - - - +
93A ALA* 1.3 66.8 + - - +
94A LEU 3.2 0.3 + - - -
95A ALA* 3.2 1.0 + - - -
96A ARG* 2.9 68.4 + - + +
113A MET* 3.4 24.2 - - + +
118A LEU* 3.8 22.2 - - + +
121A GLN* 3.7 37.9 - - + +
122A CYS* 4.4 3.1 - - + -
319A GLU* 5.7 0.2 - - - +
890A MES 4.0 15.7 - - - +
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Residues in contact with ALA 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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87A TRP* 5.1 2.9 - - + -
88A PRO 5.0 3.1 - - - +
89A LYS 3.0 11.9 + - - +
90A GLY* 3.6 9.0 - - - +
92A LEU* 1.3 76.8 - - - +
94A LEU* 1.3 61.3 + - - +
97A ALA* 3.2 19.9 + - - +
314A LEU* 3.7 20.6 - - + -
319A GLU* 3.3 45.6 - - + +
322A VAL* 4.7 0.4 - - - +
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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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77A ILE* 3.7 25.5 - - + +
80A THR* 4.7 1.3 - - - +
83A ASN* 3.3 33.4 - - - +
90A GLY 3.0 19.3 + - - +
91A ASP* 3.5 3.4 - - - +
93A ALA* 1.3 74.3 - - - +
95A ALA* 1.3 65.9 + - - +
97A ALA* 3.2 2.1 + - - +
98A ALA* 2.9 24.1 + - - +
105A PHE* 3.4 23.6 - - + -
310A THR* 4.4 6.1 - - - +
311A LEU* 3.9 15.3 - - + -
314A LEU* 3.8 18.4 - - + -
322A VAL* 3.6 26.9 - - + -
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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 ASP 3.1 11.9 + - - +
92A LEU 3.8 3.1 - - - +
94A LEU* 1.3 78.2 - - - +
96A ARG* 1.3 58.5 + - - +
98A ALA* 3.4 1.7 + - - +
99A THR* 2.8 35.3 + - - -
105A PHE* 3.6 34.6 - - + +
118A LEU* 3.8 20.6 - - + -
122A CYS* 3.9 13.5 - - - -
126A LEU* 4.3 1.3 - - + -
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Residues in contact with ARG 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 LEU* 2.9 45.7 + - + +
93A ALA 4.1 0.2 - - - +
95A ALA* 1.3 74.8 - - - +
97A ALA* 1.3 59.9 + - - +
99A THR* 3.8 5.6 - - - -
100A LYS* 2.9 38.7 + - + +
121A GLN* 3.0 36.9 + - - +
122A CYS* 4.5 9.2 - - - +
319A GLU* 3.9 30.0 + - - +
890A MES 4.4 13.1 + - - -
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Residues in contact with ALA 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 ALA 3.2 11.1 + - - +
94A LEU 3.2 1.9 + - - +
96A ARG* 1.3 76.0 - - - +
98A ALA* 1.3 61.4 + - - +
100A LYS* 3.4 4.0 + - - +
101A ALA* 2.9 29.6 + - - +
319A GLU* 4.2 2.9 - - + +
322A VAL* 3.3 37.9 - - + -
323A ASP* 3.2 30.1 - - - +
326A LEU* 3.5 4.5 - - + +
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Residues in contact with ALA 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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77A ILE* 3.8 12.1 - - + -
94A LEU 2.9 15.8 + - - +
95A ALA 3.5 4.9 - - - +
97A ALA* 1.3 77.9 - - - +
99A THR* 1.3 63.8 + - - +
101A ALA* 2.9 12.1 + - - +
102A GLY 2.9 10.0 + - - -
103A ILE* 3.1 31.9 + - + +
104A PRO 3.7 13.7 - - - +
105A PHE* 3.9 11.4 - - + -
326A LEU* 4.1 6.2 - - - +
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Residues in contact with THR 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* 2.8 20.8 + - - +
96A ARG* 3.8 4.9 - - - -
98A ALA* 1.3 75.9 - - - +
100A LYS* 1.3 63.9 + - + +
102A GLY* 3.1 13.8 + - - +
103A ILE 3.8 5.1 + - - +
105A PHE* 5.7 0.7 - - - +
122A CYS* 3.3 12.9 - - - -
123A ASP* 4.1 11.4 - - - +
124A GLY* 3.2 39.1 - - - +
125A ASP 4.6 0.5 + - - -
126A LEU* 5.2 1.7 - - - +
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Residues in contact with LYS 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 ARG* 2.9 29.1 + - + +
97A ALA* 3.7 4.3 - - - +
98A ALA 3.2 0.2 - - - -
99A THR* 1.3 79.1 - - + +
101A ALA* 1.3 59.2 + - - +
102A GLY 3.5 0.5 + - - -
319A GLU* 2.6 29.7 + - - -
323A ASP* 3.0 36.7 + - - +
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Residues in contact with ALA 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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72A SER* 2.5 30.8 + - - -
73A MET* 4.2 18.7 - - + +
97A ALA 2.9 18.8 + - - +
98A ALA 2.9 4.7 + - - +
100A LYS* 1.3 75.7 - - - +
102A GLY* 1.3 52.6 + - - +
103A ILE* 3.4 3.8 - - + -
326A LEU* 3.7 24.2 - - + -
330A LYS* 4.9 3.5 + - - -
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Residues in contact with GLY 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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71A GLN* 3.4 9.4 - - - +
72A SER* 3.2 26.7 + - - -
98A ALA 2.9 2.8 + - - -
99A THR* 3.1 13.7 + - - -
100A LYS 3.2 0.8 - - - -
101A ALA* 1.3 80.7 - - - +
103A ILE* 1.3 59.5 + - - +
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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