Contacts of the helix formed by residues 100 - 110 (chain A) in PDB entry 4I0A
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 TYR 100 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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37A ALA* 3.1 29.6 - - - +
38A GLU* 2.9 18.5 + - - +
39A THR 3.2 28.9 - - - -
40A LEU* 3.6 10.5 - - + -
72A GLY 2.4 27.5 + - - -
75A GLY* 3.2 37.6 + - - -
76A LEU* 3.5 33.1 - - + +
79A GLU* 6.4 0.2 - - - -
83A ARG* 3.0 11.7 + - - -
99A SER* 1.3 70.8 - - - +
101A LYS* 1.3 53.6 + - - +
103A PHE* 3.0 3.8 + - - +
104A ARG* 2.8 61.5 + - - +
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Residues in contact with LYS 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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99A SER* 3.2 8.1 - - - +
100A TYR* 1.3 79.5 - - - +
102A LYS* 1.3 61.2 + - - +
104A ARG* 3.4 20.7 + - - +
105A GLN* 3.1 46.2 + - + +
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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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18A HIS* 3.0 58.1 - - - +
98A ILE* 3.8 14.3 - - + +
99A SER* 3.0 23.8 + - - +
101A LYS* 1.3 75.3 - - - +
103A PHE* 1.4 63.7 + - - +
105A GLN* 3.2 23.0 + - + +
106A LEU* 3.0 25.8 + - + +
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Residues in contact with PHE 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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15A PHE* 3.6 32.5 - + - -
40A LEU* 3.6 23.1 - - + -
70A PHE* 4.4 3.8 - + - -
76A LEU* 3.7 26.9 - - + -
98A ILE* 4.0 11.6 - - + +
99A SER 2.9 14.2 + - - +
100A TYR* 3.0 11.9 + - - +
102A LYS* 1.4 77.4 - - - +
104A ARG* 1.3 56.8 + - - +
106A LEU* 3.0 8.6 + - + +
107A ILE* 2.9 51.6 + - + +
113A ILE* 3.8 41.5 - - + -
114A LEU* 4.9 2.2 - - - -
117A LEU* 3.9 12.8 - - + -
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Residues in contact with ARG 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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75A GLY 4.7 1.8 + - - -
76A LEU* 3.3 35.7 + - + +
77A PHE 5.6 0.4 - - - -
78A GLU 5.1 0.2 - - - -
79A GLU* 5.0 16.0 - - - +
100A TYR* 2.8 44.0 + - - +
101A LYS* 3.6 32.8 - - - +
103A PHE* 1.3 74.0 - - - +
105A GLN* 1.3 60.7 + - + +
107A ILE* 3.4 18.8 + - + +
108A GLN* 3.5 19.5 + - - +
115B MET* 4.7 18.3 - - + +
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Residues in contact with GLN 105 (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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101A LYS* 3.1 41.9 + - + +
102A LYS* 3.2 25.4 + - - +
104A ARG* 1.3 73.1 - - + +
106A LEU* 1.3 67.6 - - + +
108A GLN* 3.0 22.2 + - - +
109A VAL* 3.3 11.6 + - - +
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Residues in contact with LEU 106 (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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14A TRP* 3.3 35.6 - - + -
15A PHE* 4.0 27.8 - - + -
18A HIS* 3.8 36.1 - - + +
98A ILE* 3.9 22.4 - - + -
102A LYS* 3.0 21.1 + - - +
103A PHE* 3.0 11.1 + - + +
105A GLN* 1.3 78.1 - - + +
107A ILE* 1.3 63.7 + - - +
109A VAL* 3.1 7.3 + - + +
110A ASN 3.0 21.0 + - - +
113A ILE* 4.5 5.6 - - + -
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Residues in contact with ILE 107 (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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76A LEU* 4.7 4.5 - - + -
103A PHE* 2.9 48.7 + - + +
104A ARG* 3.6 16.2 - - + +
105A GLN 3.2 0.4 - - - -
106A LEU* 1.3 75.1 - - - +
108A GLN* 1.3 70.4 + - - +
110A ASN 4.1 7.2 - - - -
111A PRO* 3.2 31.3 - - + +
113A ILE* 4.2 4.9 - - + -
114A LEU* 4.0 44.6 - - + -
111B PRO* 5.1 6.4 - - + +
115B MET* 4.1 22.0 - - + -
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Residues in contact with GLN 108 (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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104A ARG 3.5 15.4 - - - +
105A GLN* 3.0 12.4 + - - +
107A ILE* 1.3 86.3 + - - +
109A VAL* 1.3 64.5 + - + +
111A PRO* 4.9 3.8 - - - +
111B PRO* 4.5 16.9 - - - +
112B ASP* 4.4 13.4 + - - +
115B MET* 5.8 2.6 - - - +
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Residues in contact with VAL 109 (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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14A TRP* 3.9 23.3 - - + +
105A GLN 3.3 11.8 + - - +
106A LEU* 3.1 11.5 + - + +
108A GLN* 1.3 80.2 - - + +
110A ASN* 1.3 61.0 + - + +
111A PRO* 4.3 2.5 - - - +
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Residues in contact with ASN 110 (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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11A THR* 4.0 26.6 + - - +
14A TRP* 3.8 19.7 - - + -
106A LEU 3.0 7.7 + - - +
107A ILE 3.4 2.7 - - - -
108A GLN 3.4 0.2 - - - -
109A VAL* 1.3 81.7 - - + +
111A PRO* 1.4 67.3 - - - +
112A ASP* 3.0 29.4 + - - +
113A ILE* 3.4 22.0 + - - +
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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