Contacts of the helix formed by residues 101 - 109 (chain A) in PDB entry 2AGA
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 SER 101 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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65A THR* 5.2 16.6 - - - +
68A GLN* 6.1 4.8 - - - +
98A LEU* 4.0 18.7 + - - +
99A PHE 2.6 8.3 + - - +
100A ASN* 1.3 76.9 - - - +
102A PRO* 1.4 60.6 - - - +
103A GLU* 3.1 7.0 + - - +
104A TYR* 3.1 36.6 + - - +
105A GLN* 2.6 32.6 + - - +
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Residues in contact with PRO 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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68A GLN* 5.7 6.3 - - + +
100A ASN 2.7 9.8 - - - +
101A SER* 1.4 82.9 - - - +
103A GLU* 1.3 69.7 + - + +
105A GLN* 4.0 7.6 - - + +
106A ARG* 3.0 31.5 + - - +
165A TYR* 4.8 18.2 - - + +
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Residues in contact with GLU 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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61A GLU* 5.0 11.6 - - - +
65A THR* 3.9 18.2 + - - -
101A SER* 3.1 6.3 - - - +
102A PRO* 1.3 85.9 - - + +
104A TYR* 1.3 60.2 + - + +
106A ARG* 3.8 2.5 - - - +
107A LEU* 2.9 40.2 + - + +
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Residues in contact with TYR 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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65A THR* 5.7 8.3 - - + -
97A ILE* 4.4 19.0 - - + +
98A LEU 5.2 0.2 - - - -
99A PHE 5.2 0.7 - - - +
101A SER* 3.1 29.2 + - - +
103A GLU* 1.3 79.3 - - + +
105A GLN* 1.3 60.6 + - - +
107A LEU* 3.0 11.5 + - + +
108A ARG 2.8 26.0 + - - -
109A ILE* 3.0 38.6 + - + +
171A LYS* 3.8 23.6 + - - -
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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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99A PHE* 2.5 66.6 + - - +
100A ASN 3.3 3.2 + - - +
101A SER 2.6 25.1 + - - +
102A PRO* 4.1 5.8 - - + +
104A TYR* 1.3 74.3 - - - +
106A ARG* 1.3 62.7 + - - +
108A ARG* 3.0 4.0 + - - -
109A ILE* 3.0 36.2 + - + +
111A PRO* 5.1 1.0 - - - +
161A GLN* 3.1 19.4 + - - +
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Residues in contact with ARG 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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102A PRO 3.0 21.5 + - - +
103A GLU* 3.8 4.0 - - - +
105A GLN* 1.3 73.0 - - - +
107A LEU* 1.3 70.8 + - + +
108A ARG* 3.0 12.3 + - - +
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Residues in contact with LEU 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 GLU* 2.9 28.0 + - + +
104A TYR* 3.0 12.8 + - + +
106A ARG* 1.3 84.5 - - + +
108A ARG* 1.3 76.7 + - - +
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Residues in contact with ARG 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 TYR 2.8 3.8 + - - -
105A GLN 3.4 4.0 - - - -
106A ARG 3.0 9.2 + - - +
107A LEU* 1.3 96.0 - - - +
109A ILE* 1.3 64.4 + - - +
110A ASP 4.2 0.8 + - - -
113A ASN* 4.6 8.5 + - - -
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Residues in contact with ILE 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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97A ILE* 5.8 0.4 - - + -
99A PHE* 3.5 26.5 - - + +
104A TYR* 3.0 48.3 + - + +
105A GLN* 3.0 39.4 + - + +
108A ARG* 1.3 78.2 - - - +
110A ASP* 1.3 65.6 + - - +
111A PRO* 4.5 0.2 - - - +
114A GLU* 4.3 18.4 - - - +
169A VAL* 4.8 16.2 - - + -
171A LYS* 5.2 6.5 - - - +
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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