Contacts of the helix formed by residues 97 - 110 (chain A) in PDB entry 2J25
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 97 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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20A ALA* 3.6 10.0 - - - +
95A ALA 4.0 0.8 + - - -
96A LEU* 1.3 71.0 - - - +
98A PRO* 1.3 77.4 - - - +
99A PRO* 3.1 12.4 - - - +
100A ALA* 2.7 17.5 + - - +
101A GLN 3.0 6.4 + - - -
409A ASP* 2.7 34.3 + - - -
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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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96A LEU 3.5 3.3 - - - +
97A SER* 1.3 82.2 - - - +
99A PRO* 1.3 70.3 - - + +
101A GLN* 3.0 29.5 + - + +
102A ASN* 3.0 23.8 + - - +
163A ARG* 5.2 1.8 - - - +
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Residues in contact with PRO 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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20A ALA* 3.2 25.1 - - + +
97A SER* 3.1 16.4 - - - +
98A PRO* 1.3 96.8 - - + +
100A ALA* 1.3 60.5 + - - +
102A ASN* 3.1 17.8 + - + +
103A LEU* 3.2 17.0 + - - +
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Residues in contact with ALA 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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19A ASN 3.7 26.0 - - - +
20A ALA* 3.8 5.8 - - - +
96A LEU* 3.6 17.0 - - + -
97A SER* 2.7 17.1 + - - +
99A PRO* 1.3 72.3 - - - +
101A GLN* 1.3 64.4 + - - +
103A LEU 3.2 2.0 + - - +
104A LEU* 3.0 19.1 + - - +
409A ASP* 3.6 21.1 - - - +
411A PHE* 3.4 12.1 - - + -
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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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93A ILE* 3.4 21.9 - - + +
94A LEU* 3.1 34.7 + - - +
96A LEU* 2.6 33.2 + - - +
97A SER 3.0 5.5 + - - +
98A PRO* 3.0 23.5 + - + +
100A ALA* 1.3 75.9 - - - +
102A ASN* 1.3 59.1 + - - +
104A LEU* 3.3 8.9 + - - +
105A LEU* 3.0 29.6 + - - +
160A LEU* 4.6 0.9 - - - +
163A ARG* 2.9 36.1 + - - +
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Residues in contact with ASN 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* 3.0 26.9 + - - +
99A PRO* 3.1 9.4 + - - +
101A GLN* 1.3 74.8 - - - +
103A LEU* 1.3 57.8 + - + +
105A LEU* 3.8 8.2 - - - +
106A LYS* 2.7 50.9 + - + +
163A ARG* 3.2 26.0 + - - +
167A LEU* 4.5 12.7 - - + +
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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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2A ARG* 5.8 1.1 - - - +
19A ASN 3.3 23.6 - - - +
20A ALA 3.7 12.6 - - - +
21A THR 4.0 2.9 - - - -
22A TYR* 3.6 28.5 - - - +
23A CYS* 3.7 21.2 - - + +
99A PRO 3.2 11.7 + - - +
100A ALA 3.2 5.4 + - - +
102A ASN* 1.3 77.8 - - + +
104A LEU* 1.3 55.6 + - - +
106A LYS* 3.9 18.7 - - + +
107A SER* 3.0 30.3 + - - -
411A PHE* 3.7 6.5 - - + -
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Residues in contact with LEU 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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93A ILE* 3.8 37.2 - - + -
96A LEU* 3.8 23.3 - - + -
100A ALA 3.0 12.7 + - - +
101A GLN* 3.4 10.1 - - - +
102A ASN 3.2 0.2 - - - -
103A LEU* 1.3 73.9 - - - +
105A LEU* 1.3 68.3 + - + +
107A SER* 2.9 21.6 - - - -
108A TYR* 3.3 27.2 + - + +
383A LEU* 6.3 0.2 - - + -
384A ALA* 4.5 2.7 - - + -
402A ILE* 3.8 31.2 - - + -
404A VAL* 4.2 7.6 - - + -
411A PHE* 3.3 18.2 - - + -
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Residues in contact with LEU 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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85A MET* 4.9 7.6 - - + -
93A ILE* 4.4 27.6 - - + -
101A GLN 3.0 17.1 + - - +
102A ASN* 3.1 8.3 + - - +
104A LEU* 1.3 77.4 - - + +
106A LYS* 1.3 70.0 + - - +
107A SER 3.0 0.5 + - - -
108A TYR 3.0 2.1 + - - -
109A PHE* 2.8 49.8 + - + +
160A LEU* 4.2 11.7 - - + +
163A ARG* 3.8 50.5 - - + +
164A ALA* 4.4 9.0 - - + +
167A LEU* 4.7 10.1 - - + -
383A LEU* 5.9 0.4 - - + -
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Residues in contact with LYS 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 ASN* 2.7 33.3 + - + +
103A LEU* 3.9 17.0 - - + +
105A LEU* 1.3 74.4 - - - +
107A SER* 1.3 62.3 + - - +
110A SER* 2.9 42.7 + - - +
112A GLU* 3.4 34.0 + - + +
113A GLY* 3.2 8.1 - - - -
167A LEU* 3.1 30.3 - - + +
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Residues in contact with SER 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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23A CYS* 3.6 7.3 - - - -
24A ASP 4.6 1.7 + - - -
103A LEU 3.0 17.1 + - - -
104A LEU* 2.9 18.6 - - - -
105A LEU 3.0 0.4 - - - -
106A LYS* 1.3 76.5 - - - +
108A TYR* 1.3 54.8 + - - +
112A GLU 5.4 0.4 - - - -
113A GLY* 2.9 7.7 - - - -
114A ILE 2.8 24.3 + - - -
402A ILE* 4.4 5.2 - - - -
411A PHE* 4.4 0.2 - - - -
413A LYS* 3.0 30.6 + - - +
417A PHE* 3.5 23.7 - - - -
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Residues in contact with TYR 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 LEU* 3.3 20.6 + - + -
105A LEU 3.0 2.7 + - - +
107A SER* 1.3 81.6 - - - +
109A PHE* 1.3 73.5 + + + +
110A SER 3.8 0.2 - - - -
114A ILE* 3.5 5.4 - - + +
115A GLY 3.0 8.2 + - - -
116A TYR* 2.7 72.3 + + + +
380A ASP* 4.8 0.7 + - - -
383A LEU* 2.7 53.8 + - + -
401A PRO* 3.2 27.7 - - + +
402A ILE* 3.5 18.8 - - + +
417A PHE* 3.7 24.0 - + - -
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Residues in contact with PHE 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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85A MET* 5.4 0.9 - - + -
105A LEU* 2.8 40.7 + - + +
108A TYR* 1.3 88.3 - + + +
110A SER* 1.3 64.0 + - - +
115A GLY* 3.7 10.3 - - - -
116A TYR* 3.6 33.6 - - + +
118A ILE 4.2 2.0 - - - -
119A ILE* 3.4 42.2 - - + -
164A ALA* 3.7 40.2 - - + +
167A LEU* 4.7 1.8 - - + -
168A ALA* 3.2 21.1 - - + +
169A GLN 3.7 3.5 + - - -
170A ARG 5.2 0.5 + - - -
172A VAL* 4.5 7.9 - - + -
383A LEU* 4.3 22.9 - - + -
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Residues in contact with SER 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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105A LEU 4.0 0.2 + - - -
106A LYS* 2.9 38.4 + - - -
109A PHE* 1.3 81.2 - - - +
111A GLU* 1.3 55.9 + - - +
112A GLU* 2.7 34.9 + - - +
113A GLY* 2.6 29.1 + - - -
115A GLY 3.4 3.8 + - - -
167A LEU* 3.5 19.5 + - - -
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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