Contacts of the helix formed by residues 103 - 113 (chain A) in PDB entry 3NA0
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 ASP 103 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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87A PRO* 4.8 1.5 + - + -
102A ILE* 1.3 80.6 - - + +
104A PRO* 1.4 71.6 - - - +
105A GLU* 2.6 39.7 + - - +
106A ASP* 2.9 35.6 + - - +
107A VAL* 3.0 11.8 + - - +
405A ARG* 2.7 26.9 + - - +
428A PHE* 3.5 27.3 - - + -
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Residues in contact with PRO 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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102A ILE 3.6 6.4 - - - +
103A ASP* 1.4 88.1 - - - +
105A GLU* 1.3 54.3 + - - +
107A VAL* 3.5 14.6 - - + +
108A ALA* 3.0 27.5 + - - +
422A LEU* 4.2 9.6 - - + -
428A PHE* 3.7 19.3 - - + -
449A TYR* 3.5 26.7 - - + +
450A PHE* 3.5 14.9 - - + +
451A ARG* 3.5 34.8 - - - +
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Residues in contact with GLU 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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103A ASP* 2.6 25.2 + - - +
104A PRO* 1.3 71.3 - - - +
106A ASP* 1.3 63.3 + - - +
108A ALA* 3.5 4.5 + - - +
109A LEU* 3.4 31.5 + - + +
405A ARG* 5.8 0.9 - - - +
449A TYR* 3.8 28.7 + - + -
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Residues in contact with ASP 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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87A PRO 4.6 4.7 - - - +
88A ILE* 5.3 0.2 - - - +
101A VAL* 4.2 25.9 - - + +
103A ASP* 2.9 22.1 + - - +
105A GLU* 1.3 76.6 - - - +
107A VAL* 1.3 66.0 + - - +
109A LEU* 3.2 9.0 + - - +
110A LEU* 2.9 23.1 + - - +
404A LEU* 3.8 23.0 - - + +
405A ARG* 3.2 47.8 + - - +
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Residues in contact with VAL 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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101A VAL* 4.7 5.8 - - + -
102A ILE 4.7 3.1 - - - +
103A ASP 3.0 17.4 + - - +
104A PRO* 3.5 16.2 - - + +
106A ASP* 1.3 77.5 - - - +
108A ALA* 1.3 62.5 + - - +
110A LEU* 3.1 8.2 + - - +
111A PHE* 3.0 49.0 + - + -
417A VAL* 3.6 32.1 - - + -
422A LEU* 5.1 0.9 - - + -
450A PHE* 3.9 14.1 - - + -
453A LEU* 4.1 17.9 - - + -
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Residues in contact with ALA 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 PRO 3.0 17.4 + - - +
105A GLU* 3.7 9.6 - - - +
106A ASP 3.2 0.2 - - - -
107A VAL* 1.3 75.9 - - - +
109A LEU* 1.3 58.9 + - + +
111A PHE* 3.6 1.4 + - - +
112A LYS* 2.9 37.8 + - + +
449A TYR* 3.5 29.2 - - + +
450A PHE* 3.8 25.1 - - + -
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Residues in contact with LEU 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 GLU* 3.4 24.2 + - + +
106A ASP* 3.2 13.1 + - - +
108A ALA* 1.3 74.6 - - + +
110A LEU* 1.3 68.6 + - - +
112A LYS* 3.3 16.0 + - + +
113A SER* 3.4 14.7 + - - -
402A LEU* 4.3 13.1 - - + +
403A VAL 4.4 7.2 - - - +
404A LEU* 3.7 23.8 - - + -
405A ARG 5.9 0.7 - - - +
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Residues in contact with LEU 110 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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101A VAL* 5.4 1.1 - - + -
106A ASP 2.9 12.9 + - - +
107A VAL* 3.1 8.0 + - - +
109A LEU* 1.3 75.4 - - - +
111A PHE* 1.3 80.3 + - + +
113A SER* 3.2 18.9 + - - -
114A GLU* 3.6 6.8 + - - +
394A LEU 6.3 0.2 - - - -
395A GLN 5.7 0.7 - - - -
396A ARG* 4.1 24.7 - - + +
398A LEU* 3.6 29.8 - - + +
402A LEU* 4.3 11.6 - - + +
404A LEU* 5.1 4.5 - - + -
415A VAL* 4.1 27.6 - - + +
417A VAL* 3.8 29.8 - - + -
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Residues in contact with PHE 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 VAL* 3.0 45.9 + - + +
108A ALA 4.4 0.2 - - - +
110A LEU* 1.3 87.7 - - + +
112A LYS* 1.3 63.4 + - - +
113A SER 3.4 0.2 - - - -
114A GLU* 3.1 39.2 - - - +
394A LEU* 3.9 32.5 - - + -
396A ARG* 3.9 24.9 - - + -
417A VAL* 4.5 2.2 - - + -
450A PHE* 4.2 9.9 - + + -
453A LEU* 4.8 1.8 - - + -
457A TRP* 3.2 75.9 - + + -
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Residues in contact with LYS 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 ALA* 2.9 27.0 + - + +
109A LEU* 3.4 15.9 - - + +
110A LEU 3.1 0.2 - - - -
111A PHE* 1.3 79.5 - - - +
113A SER* 1.3 56.3 + - - +
114A GLU 3.2 6.3 + - - +
449A TYR* 5.4 1.4 + - - +
450A PHE* 5.4 7.0 - - + -
457A TRP* 5.2 7.2 - - + -
80C LEU 5.3 0.4 - - - -
81C ALA* 2.9 41.2 + - - +
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Residues in contact with SER 113 (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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109A LEU 3.4 8.4 + - - -
110A LEU 3.2 12.4 + - - -
112A LYS* 1.3 76.5 - - - +
114A GLU* 1.3 66.2 - - - +
115A GLY* 3.5 2.1 + - - -
398A LEU* 4.8 6.8 - - - +
399A VAL* 5.3 7.3 + - - +
400A ASN* 5.3 15.9 + - - -
401A ASP 5.9 1.3 - - - -
402A LEU* 4.0 23.1 - - - +
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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