Contacts of the helix formed by residues 98 - 109 (chain A) in PDB entry 2FOL
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 ASN 98 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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16A ASP* 2.7 39.9 + - - +
94A GLU* 2.9 37.7 + - - +
95A SER 3.9 3.4 - - - +
96A PHE 3.2 0.8 - - - -
97A ASN* 1.3 74.0 - - - +
99A VAL* 1.3 64.6 + - - +
100A LYS 3.1 0.9 - - - -
101A GLN* 3.1 30.9 + - + +
102A TRP* 2.9 22.1 + - - +
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Residues in contact with VAL 99 (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 VAL* 3.8 18.8 - - + -
87A VAL 4.5 1.8 - - - +
88A TYR* 3.9 15.0 - - + -
95A SER 3.6 10.4 + - - +
96A PHE* 3.1 17.9 + - + +
97A ASN 3.0 0.6 + - - -
98A ASN* 1.3 75.9 - - - +
100A LYS* 1.3 66.0 + - - +
102A TRP* 3.0 19.2 + - + +
103A LEU* 3.1 25.5 + - + +
118A LEU* 3.7 28.9 - - + -
139A PHE* 3.7 26.7 - - + -
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Residues in contact with LYS 100 (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 ASN 3.1 15.0 + - - +
99A VAL* 1.3 80.4 - - - +
101A GLN* 1.3 88.2 + - - +
103A LEU* 3.5 16.2 + - - +
104A GLN* 3.5 30.5 + - - +
139A PHE* 4.9 9.0 - - + -
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Residues in contact with GLN 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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97A ASN 4.0 1.4 - - - +
98A ASN* 3.1 30.2 + - + +
100A LYS* 1.3 103.1 + - - +
102A TRP* 1.3 63.6 + - + +
103A LEU 3.0 1.8 - - - -
104A GLN* 2.9 38.5 + - - +
105A GLU* 3.1 17.3 + - + +
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Residues in contact with TRP 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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14A ILE* 2.9 41.1 - - + +
15A GLY* 3.3 32.3 - - - -
16A ASP* 2.8 34.4 + - - +
78A TYR* 4.6 4.5 - - - -
86A VAL* 3.8 17.9 - - + -
87A VAL 5.1 0.4 - - - -
95A SER 5.1 1.6 - - - -
98A ASN* 2.9 27.6 + - + +
99A VAL* 3.0 12.1 + - + +
101A GLN* 1.3 81.5 - - + +
103A LEU* 1.3 58.2 + - - +
105A GLU* 3.5 26.3 - - + +
106A ILE* 3.3 20.7 - - - +
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Residues in contact with LEU 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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86A VAL* 4.2 20.0 - - + -
99A VAL* 3.1 29.8 + - + +
100A LYS* 3.8 9.4 - - - +
101A GLN 3.0 1.0 - - - -
102A TRP* 1.3 75.5 - - - +
104A GLN* 1.3 59.9 + - + +
105A GLU 3.1 2.0 - - - -
106A ILE* 3.2 6.2 + - + +
107A ASP* 2.9 36.0 + - - +
116A LYS* 3.8 29.6 - - + +
139A PHE* 4.5 3.6 - - + -
143A LEU* 3.5 33.0 - - + -
145A ILE* 4.3 12.1 - - + -
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Residues in contact with GLN 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 LYS* 3.5 38.7 + - - +
101A GLN* 2.9 24.4 + - - +
103A LEU* 1.3 74.8 - - + +
105A GLU* 1.3 60.6 + - + +
107A ASP* 3.4 9.3 + - - +
108A ARG* 3.0 27.5 + - - +
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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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78A TYR* 3.5 26.3 + - - +
101A GLN* 3.1 19.4 + - + +
102A TRP* 3.5 29.3 - - + +
104A GLN* 1.3 75.5 - - + +
106A ILE* 1.3 57.7 + - - +
108A ARG* 3.1 4.6 + - - +
109A TYR* 2.8 69.7 + - - +
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Residues in contact with ILE 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 ILE* 3.3 28.9 - - + -
78A TYR* 4.5 4.3 - - + -
84A ILE* 3.6 22.4 - - + -
86A VAL* 3.6 15.3 - - + -
102A TRP 3.3 12.8 + - - +
103A LEU* 3.2 11.3 + - + +
105A GLU* 1.3 80.5 - - - +
107A ASP* 1.3 64.6 + - - +
110A ALA* 3.1 33.9 + - + +
111A SER 5.1 0.2 - - - +
114A VAL* 3.4 30.9 - - + +
116A LYS* 4.0 31.0 - - + +
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Residues in contact with ASP 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 LEU* 2.9 17.6 + - - +
104A GLN* 3.7 10.5 - - - +
105A GLU 3.2 0.4 - - - -
106A ILE* 1.3 79.2 - - - +
108A ARG* 1.3 60.5 + - - +
110A ALA 4.5 6.0 - - - +
112A GLU* 6.2 0.2 - - - -
116A LYS* 3.5 22.4 + - - -
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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 GLN 3.0 17.0 + - - +
105A GLU* 3.1 4.9 + - - +
107A ASP* 1.3 79.4 - - - +
109A TYR* 1.3 104.7 + - + +
110A ALA 3.7 2.6 + - - +
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Residues in contact with TYR 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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78A TYR* 2.8 51.7 - + + +
79A ARG* 4.5 2.9 - - - -
105A GLU* 2.8 44.7 + - - +
106A ILE 3.7 0.7 - - - -
108A ARG* 1.3 124.8 + - + +
110A ALA* 1.3 63.7 + - - +
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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