Contacts of the helix formed by residues 103 - 112 (chain A) in PDB entry 5I74
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 TRP 103 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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99A LEU* 2.9 53.6 + - + +
100A GLY* 3.8 2.3 - - - +
102A VAL* 1.3 76.9 - - - +
104A ARG* 1.3 126.3 + - + +
105A PHE 3.2 2.0 - - - -
106A PRO* 3.0 14.5 - - - +
107A TYR* 3.4 17.1 + + + +
379A ILE* 4.9 4.2 - - - +
401A ALA* 4.2 7.9 - - + -
402A GLY* 3.5 44.0 - - - +
403A PRO* 4.9 9.1 - - + +
405A LEU* 5.2 13.6 - - + +
406A LEU* 3.9 36.3 - - + -
493A GLU* 5.8 2.2 - - - -
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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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100A GLY* 2.9 28.4 + - - +
103A TRP* 1.3 116.5 - - + +
105A PHE* 1.3 62.2 + - - +
107A TYR* 3.6 3.0 + - - +
108A ILE* 3.2 27.2 + - + +
332A GLN* 3.9 20.6 - - - +
490A LYS* 5.7 2.8 - - - +
493A GLU* 3.2 33.1 + - - +
494A GLU* 4.4 14.6 + - - -
703A D12 3.8 46.5 - - + +
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Residues in contact with PHE 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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100A GLY 3.1 7.3 + - - +
101A ASN 4.0 9.2 - - - +
104A ARG* 1.3 74.2 - - - +
106A PRO* 1.3 72.3 - - + +
108A ILE* 3.3 9.5 - - + +
109A CYS* 2.9 34.4 + - + +
117A PHE* 4.4 9.9 - + - -
118A LEU* 4.4 21.5 - - + -
121A TYR* 3.9 47.8 - + + -
312A TYR* 3.7 20.4 - - - -
332A GLN* 3.9 18.6 - - + +
369A CYS 5.3 0.7 - - - -
372A SER* 3.4 41.5 - - - +
373A PHE* 4.0 8.1 - + + -
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Residues in contact with PRO 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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101A ASN 3.8 4.3 - - - +
102A VAL 3.2 24.0 - - - +
103A TRP* 3.0 15.9 - - - +
105A PHE* 1.3 92.2 - - + +
107A TYR* 1.3 56.1 + - - +
109A CYS* 3.3 2.4 + - - +
110A ALA* 2.9 23.9 + - - +
312A TYR* 4.0 10.0 - - + -
375A SER 4.1 1.3 - - - +
376A GLY* 3.4 28.7 - - - +
379A ILE* 4.5 8.7 - - + -
380A PHE* 3.4 32.2 - - + -
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Residues in contact with TYR 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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103A TRP* 3.4 16.4 + + + +
104A ARG* 4.0 4.5 - - - +
105A PHE 3.3 0.8 - - - -
106A PRO* 1.3 78.0 - - - +
108A ILE* 1.3 70.5 + - + +
110A ALA* 3.0 16.6 + - + +
111A GLN* 3.0 53.9 + - + +
380A PHE* 4.7 5.4 - + - -
398A ALA* 3.3 32.3 - - + -
399A LYS* 3.9 9.7 + - - -
401A ALA* 3.5 33.9 - - + +
405A LEU* 4.7 15.9 - - + -
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Residues in contact with ILE 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* 3.2 20.2 + - + +
105A PHE* 3.3 13.2 - - - +
107A TYR* 1.3 87.4 - - + +
109A CYS* 1.3 64.0 + - - +
111A GLN* 4.2 8.1 - - - +
112A ASN* 3.4 38.2 + - - +
117A PHE* 4.2 18.5 - - + -
328A ASP* 3.6 41.1 - - + +
332A GLN* 4.5 19.5 - - + +
703A D12 4.7 10.5 - - + -
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Residues in contact with CYS 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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105A PHE* 2.9 33.2 + - + +
106A PRO 3.5 4.3 - - - +
108A ILE* 1.3 78.6 - - - +
110A ALA* 1.3 58.6 + - - +
112A ASN 3.0 19.6 - - - +
114A GLY 3.0 32.4 + - - +
115A GLY* 4.9 2.9 - - - -
117A PHE* 3.8 23.8 - - + -
118A LEU* 4.9 10.5 - - - -
312A TYR* 3.8 27.4 - - + -
313A LEU* 6.0 0.9 - - - -
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Residues in contact with ALA 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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106A PRO 2.9 8.1 + - - +
107A TYR* 3.0 4.2 + - + +
109A CYS* 1.3 80.3 - - - +
111A GLN* 1.3 63.0 + - - +
112A ASN 3.4 0.7 + - - -
114A GLY* 3.7 14.4 + - - -
311A PHE* 3.6 38.5 - - + +
312A TYR* 4.4 5.2 - - - -
380A PHE* 3.4 33.7 - - + -
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Residues in contact with GLN 111 (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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107A TYR* 3.0 56.1 + - + +
108A ILE* 4.1 7.9 - - - +
110A ALA* 1.3 78.2 - - - +
112A ASN* 1.3 86.7 + - - +
113A GLY 4.0 0.6 + - - -
311A PHE* 5.3 6.3 - - + -
319A LYS* 3.7 17.2 + - - -
328A ASP* 5.0 3.8 + - - -
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Residues in contact with ASN 112 (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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108A ILE* 3.4 30.8 + - - +
109A CYS 3.0 11.3 - - - +
110A ALA 3.3 0.4 - - - -
111A GLN* 1.3 96.1 + - - +
113A GLY* 1.3 58.9 + - - +
114A GLY 2.9 10.1 + - - -
117A PHE* 3.1 25.5 - - + +
319A LYS* 4.4 11.7 + - - -
325A VAL* 3.6 28.2 - - + +
328A ASP* 3.5 27.5 + - - +
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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