Contacts of the helix formed by residues 97 - 115 (chain A) in PDB entry 2PMF
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 GLY 97 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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78A PHE* 3.2 28.6 + - - -
79A PHE 2.9 12.3 + - - -
95A ASP 3.9 2.4 + - - -
96A PHE* 1.3 73.6 - - - +
98A PRO* 1.3 67.5 - - - +
99A VAL 3.2 2.9 - - - -
100A GLY 2.9 2.9 + - - -
101A CYS* 2.8 33.0 + - - +
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Residues in contact with PRO 98 (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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77A ARG 6.0 0.2 - - - +
78A PHE* 3.6 22.0 - - + +
97A GLY* 1.3 84.5 - - - +
99A VAL* 1.3 66.1 + - + +
101A CYS* 3.5 6.7 + - + +
102A ALA* 3.2 22.7 + - - +
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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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77A ARG* 4.1 22.0 - - - +
78A PHE 4.3 2.2 + - - +
79A PHE* 3.4 37.9 - - + -
97A GLY 3.2 1.0 - - - -
98A PRO* 1.3 78.7 - - + +
100A GLY* 1.3 63.5 + - - +
102A ALA* 3.5 6.9 + - - +
103A LEU* 3.2 21.5 + - - +
559A PRO* 3.7 20.7 - - + +
560A PHE* 6.2 1.3 - - + -
610A ILE* 4.0 26.5 - - + -
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Residues in contact with GLY 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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79A PHE* 3.2 36.6 + - - +
96A PHE* 4.5 9.9 - - - -
97A GLY 2.9 4.6 + - - -
99A VAL* 1.3 78.2 - - - +
101A CYS* 1.3 58.2 + - - +
103A LEU* 3.3 5.0 + - - +
104A LYS* 2.8 30.4 + - - +
531A MET* 4.2 5.8 - - - +
535A PHE* 5.9 0.4 - - - -
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Residues in contact with CYS 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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96A PHE* 3.6 29.1 - - - +
97A GLY 2.8 15.7 + - - +
98A PRO* 3.7 7.9 - - + +
99A VAL 3.3 0.2 - - - -
100A GLY* 1.3 69.9 - - - +
102A ALA* 1.3 56.7 + - - +
104A LYS* 4.2 8.5 - - - -
105A ASN* 2.7 51.3 + - - +
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Residues in contact with ALA 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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98A PRO 3.2 14.4 + - - +
99A VAL* 3.7 4.7 - - - +
100A GLY 3.4 0.2 - - - -
101A CYS* 1.3 78.3 - - - +
103A LEU* 1.3 57.5 + - - +
105A ASN* 3.6 5.1 + - - +
106A ASN* 2.9 37.8 + - - +
559A PRO* 3.7 31.6 - - + +
560A PHE* 6.0 0.2 - - + -
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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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79A PHE* 3.8 10.5 - - + -
99A VAL 3.2 9.5 + - - +
100A GLY* 3.5 9.0 - - - +
102A ALA* 1.3 77.9 - - - +
104A LYS* 1.3 59.2 + - - +
106A ASN* 3.2 3.1 + - - +
107A ILE* 2.9 50.3 + - + +
531A MET* 3.7 12.1 - - + -
534A VAL* 5.3 3.4 - - + -
535A PHE* 3.5 20.6 - - + -
553A PHE* 3.5 39.5 - - + -
557A VAL* 3.6 29.8 - - + +
559A PRO* 4.5 5.6 - - + +
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Residues in contact with LYS 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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96A PHE* 4.7 25.9 - - + -
100A GLY 2.8 22.3 + - - +
101A CYS* 3.6 9.6 - - - +
103A LEU* 1.3 73.6 - - - +
105A ASN* 1.3 63.0 + - - +
107A ILE* 3.3 4.4 + - - +
108A ILE* 2.9 49.8 + - + +
274A ASN* 5.5 2.2 - - - +
293A THR* 2.7 37.0 + - - +
527A LEU* 5.9 2.7 - - + -
531A MET* 3.6 32.3 - - + -
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Residues in contact with ASN 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 CYS* 2.7 34.5 + - - +
102A ALA* 3.9 6.3 + - - +
104A LYS* 1.3 80.9 - - - +
106A ASN* 1.3 60.2 + - - +
108A ILE* 3.4 11.6 + - - +
109A GLN* 2.9 31.1 + - - +
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Residues in contact with ASN 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 ALA 2.9 25.9 + - - +
103A LEU 3.2 1.1 + - - +
105A ASN* 1.3 77.3 - - - +
107A ILE* 1.3 59.6 + - - +
109A GLN* 3.8 5.2 - - - +
110A THR* 2.8 35.5 + - - -
556A VAL 3.8 15.1 + - - +
557A VAL* 3.1 18.4 + - - +
558A ALA 2.7 30.1 + - - -
559A PRO 3.5 10.6 + - - +
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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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103A LEU* 2.9 38.7 + - + +
104A LYS* 3.3 9.2 + - - +
106A ASN* 1.3 77.5 - - - +
108A ILE* 1.3 58.8 + - + +
110A THR* 3.4 5.4 + - - -
111A TRP 3.0 16.3 + - - -
362A TYR* 2.8 36.6 + - + +
366A VAL* 3.9 22.0 - - + -
527A LEU* 4.1 21.1 - - + +
530A ILE* 4.7 5.4 - - + -
531A MET* 3.8 32.8 - - + +
534A VAL* 4.7 1.3 - - + -
557A VAL* 3.9 13.2 - - + -
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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 LYS* 2.9 45.5 + - + +
105A ASN* 3.8 11.9 - - - +
107A ILE* 1.3 77.2 - - + +
109A GLN* 1.3 58.8 + - - +
111A TRP* 3.2 8.9 + - - +
112A ARG* 3.0 51.8 + - - +
272A ILE* 4.2 18.6 - - + -
293A THR* 4.3 8.3 - - + -
527A LEU* 3.7 29.6 - - + -
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Residues in contact with GLN 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 ASN 2.9 19.7 + - - +
106A ASN* 3.8 6.5 - - - +
108A ILE* 1.3 74.1 - - - +
110A THR* 1.3 65.2 + - - +
112A ARG* 3.2 30.4 + - - +
113A GLN* 3.1 30.9 + - + +
117A GLN* 6.0 2.0 - - - +
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Residues in contact with THR 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 ASN 2.8 24.9 + - - -
107A ILE* 3.6 7.0 - - - -
109A GLN* 1.3 75.3 - - - +
111A TRP* 1.3 56.9 + - - +
113A GLN* 3.4 7.3 + - + +
114A HIS* 2.9 26.6 + - + +
362A TYR* 3.9 13.5 - - + -
365A LYS* 3.7 32.0 + - + +
366A VAL* 4.2 9.6 - - + -
556A VAL* 3.6 31.0 + - + +
557A VAL* 4.3 1.4 - - - +
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Residues in contact with TRP 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 ILE 3.0 14.5 + - - +
108A ILE* 3.3 12.8 - - - +
109A GLN 3.1 0.2 - - - -
110A THR* 1.3 75.4 - - - +
112A ARG* 1.3 62.2 + - - +
114A HIS 3.2 0.2 + - - -
115A PHE* 2.9 46.0 + + + +
116A ILE* 3.8 20.2 - - + -
270A ALA* 4.2 9.6 - - + -
272A ILE* 3.7 35.0 - - + -
295A ALA* 3.5 26.0 - - + -
296A GLU 4.3 3.4 - - - -
297A ILE* 3.6 39.5 - - + -
362A TYR* 3.4 31.6 - + - +
525A PHE* 3.3 37.0 - + + -
527A LEU* 4.8 4.9 - - + -
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Residues in contact with ARG 112 (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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108A ILE* 3.0 37.3 + - - +
109A GLN* 3.2 33.2 + - - +
111A TRP* 1.3 79.2 - - - +
113A GLN* 1.3 57.2 + - - +
116A ILE* 3.2 19.3 + - + +
117A GLN* 2.9 33.8 + - + +
123A GLU* 2.6 39.6 + - - -
272A ILE* 3.6 27.9 + - + +
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Residues in contact with GLN 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 GLN* 3.1 20.7 + - + +
110A THR* 3.7 10.8 - - + +
112A ARG* 1.3 78.5 - - - +
114A HIS* 1.3 61.8 + - - +
115A PHE 3.5 0.2 + - - -
117A GLN* 3.7 26.4 + - + +
118A GLU* 3.6 23.0 + - - +
365A LYS* 6.4 0.2 - - - +
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Residues in contact with HIS 114 (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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110A THR* 2.9 18.2 + - + +
111A TRP 3.2 3.6 + - - +
113A GLN* 1.3 77.5 - - - +
115A PHE* 1.3 90.0 + + + +
118A GLU* 3.3 7.5 - - - +
119A GLU* 4.1 1.9 - - - +
358A ARG* 2.8 77.0 + - - +
361A LEU* 3.6 8.1 - - + -
362A TYR* 3.5 30.3 + - + -
365A LYS* 3.2 30.3 + - - +
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Residues in contact with PHE 115 (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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111A TRP* 2.9 54.9 + + + +
114A HIS* 1.3 107.0 - + + +
116A ILE* 1.3 60.2 + - - +
117A GLN 3.4 1.3 - - - -
118A GLU* 3.9 0.4 - - - -
119A GLU* 2.8 42.5 + - + +
121A ILE* 3.5 5.3 - - + +
297A ILE* 3.8 30.1 - - + -
355A PHE* 5.0 12.8 - + - -
358A ARG* 3.9 30.3 - - + -
359A ILE* 4.2 5.2 - - + -
362A TYR* 3.9 10.8 - + + -
523A PRO* 5.8 0.4 - - + -
525A PHE* 3.4 22.4 - + - -
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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