Contacts of the helix formed by residues 84 - 94 (chain A) in PDB entry 2P18
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 84 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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42A VAL* 3.0 17.1 + - - -
43A ASN 3.2 20.7 - - - -
44A ALA* 4.3 0.4 - - - -
46A TYR* 4.3 8.0 - - - -
83A GLY* 1.3 77.4 - - - +
85A ASN* 1.3 59.7 + - - +
86A ALA 3.5 2.5 - - - -
87A LYS* 3.3 6.0 + - - -
88A LEU* 2.8 34.8 + - - +
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Residues in contact with ASN 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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42A VAL* 3.7 11.3 + - - +
72A ILE* 3.5 28.8 - - - +
74A SER* 2.9 27.8 + - - -
81A HIS 4.4 0.5 - - - +
82A SER* 3.1 20.0 + - - +
84A GLY* 1.3 75.9 - - - +
86A ALA* 1.3 58.1 + - - +
89A LYS* 2.9 33.4 + - - +
103A VAL* 3.7 11.9 - - + +
111A ILE* 3.6 9.7 - - - +
112A PRO* 3.0 28.9 + - + +
113A ALA* 4.0 6.1 - - + -
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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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82A SER 4.9 0.2 + - - -
83A GLY 5.6 0.4 - - - -
84A GLY 3.5 0.6 - - - -
85A ASN* 1.3 78.6 - - - +
87A LYS* 1.3 59.6 + - + +
89A LYS* 3.8 5.3 - - - +
90A ALA* 3.0 28.8 + - - +
112A PRO* 5.9 3.3 - - + +
113A ALA* 4.0 17.2 - - + +
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Residues in contact with LYS 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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44A ALA* 5.7 7.0 - - - +
46A TYR* 3.6 33.6 + - + +
79A TRP* 6.4 1.6 - - - -
83A GLY 4.9 12.8 + - - +
84A GLY* 3.3 5.9 + - - +
85A ASN 3.3 0.6 - - - -
86A ALA* 1.3 78.5 - - + +
88A LEU* 1.3 65.0 + - - +
90A ALA* 3.3 7.3 + - - +
91A GLU* 3.1 26.0 + - - +
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Residues in contact with LEU 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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39A ALA* 4.3 1.6 - - + -
42A VAL* 3.8 36.1 - - + -
46A TYR* 4.0 26.6 - - + +
49A ILE* 4.8 6.7 - - + -
50A LEU* 4.1 18.8 - - + -
69A PHE* 4.0 21.8 - - + -
72A ILE* 4.1 11.2 - - + -
84A GLY 2.8 20.8 + - - +
85A ASN 4.2 1.3 - - - +
87A LYS* 1.3 70.4 - - - +
89A LYS* 1.3 55.9 + - - +
91A GLU* 3.1 7.3 + - + +
92A LEU* 2.7 55.8 - - + +
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Residues in contact with LYS 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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72A ILE* 4.0 8.4 - - + +
85A ASN 2.9 21.3 + - - +
86A ALA* 3.8 4.5 - - - +
88A LEU* 1.3 75.7 - - - +
90A ALA* 1.3 62.7 + - - +
92A LEU* 3.2 4.8 - - - +
93A GLU* 3.0 53.1 + - - +
101A VAL* 3.2 39.0 + - + +
103A VAL* 4.0 15.2 - - + +
113A ALA* 4.8 7.7 + - + +
115A THR* 3.4 26.5 - - - +
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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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86A ALA 3.0 19.3 + - - +
87A LYS* 3.5 8.1 - - - +
88A LEU 3.2 0.2 - - - -
89A LYS* 1.3 75.9 - - - +
91A GLU* 1.3 59.9 + - + +
92A LEU 2.8 8.3 + - - -
93A GLU* 3.4 7.7 + - - +
94A ALA* 3.1 20.8 + - - +
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Residues in contact with GLU 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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46A TYR* 2.8 33.2 + - + +
47A LYS* 4.9 8.8 - - - -
50A LEU* 3.4 18.8 - - + +
87A LYS 3.1 17.8 + - - +
88A LEU* 3.1 19.5 + - + +
90A ALA* 1.3 75.0 - - + +
92A LEU* 1.3 53.7 + - + +
94A ALA* 3.7 9.0 - - - +
95A MET* 3.3 37.3 + - + +
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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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50A LEU* 4.6 3.6 - - + -
69A PHE* 3.8 49.8 - - + +
72A ILE* 4.5 2.0 - - + -
88A LEU* 2.7 54.1 - - + +
89A LYS* 3.2 5.2 - - - +
90A ALA 2.8 1.2 + - - -
91A GLU* 1.3 66.1 + - - +
93A GLU* 1.3 64.1 + - - +
94A ALA 3.2 1.0 - - - +
95A MET* 3.8 24.9 - - + +
96A ASN* 3.0 30.0 + - - +
99A VAL* 4.1 2.8 + - - +
101A VAL* 3.9 30.1 - - + -
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Residues in contact with GLU 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 LYS* 3.0 52.4 + - - +
90A ALA* 4.0 6.2 - - - +
92A LEU* 1.3 76.7 - - - +
94A ALA* 1.3 62.5 + - - +
95A MET 3.3 0.4 - - - -
96A ASN 3.5 15.6 + - - +
99A VAL* 3.7 25.2 - - + +
100A PRO* 4.9 1.9 - - - +
101A VAL* 4.1 15.1 + - + -
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Residues in contact with ALA 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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90A ALA 3.1 18.8 + - - +
91A GLU* 3.7 8.1 - - - +
93A GLU* 1.3 77.5 - - - +
95A MET* 1.3 59.1 + - - +
96A ASN 3.5 0.2 - - - -
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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