Contacts of the helix formed by residues 100 - 117 (chain A) in PDB entry 3D87
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 100 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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96A LEU* 3.9 14.4 + - - +
97A LEU* 2.3 46.4 + - - +
99A ASP* 1.3 87.1 + - - +
101A PRO* 1.3 71.0 - - - +
102A VAL* 3.6 9.5 + - - +
103A GLY 2.7 31.4 + - - -
104A GLN* 3.1 8.3 + - - -
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Residues in contact with PRO 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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24A LEU* 3.3 21.1 - - + +
27A SER* 3.5 28.7 - - - +
96A LEU* 5.4 2.2 - - + -
100A SER* 1.3 91.9 - - - +
102A VAL* 1.3 64.6 + - + +
104A GLN* 3.5 13.7 + - - +
105A LEU* 3.1 18.4 + - - +
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Residues in contact with VAL 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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24A LEU 5.8 0.2 - - - -
27A SER* 4.8 10.3 - - - +
85A LEU* 5.0 3.6 - - + +
90A PHE* 3.6 36.8 - - + +
96A LEU* 5.7 8.3 - - + -
100A SER* 3.1 8.0 - - - +
101A PRO* 1.3 79.9 - - + +
103A GLY* 1.3 67.1 + - - +
105A LEU* 2.9 25.2 - - + +
106A HIS* 3.1 8.1 + - + +
144A PHE* 6.2 0.7 - - + -
147A LEU* 4.4 28.0 - - + -
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Residues in contact with GLY 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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97A LEU 4.3 0.2 - - - -
98A PRO* 3.6 27.6 - - - -
100A SER* 2.7 23.0 + - - -
102A VAL* 1.3 74.3 - - - +
104A GLN* 1.3 63.3 + - - -
105A LEU 2.8 1.7 + - - -
106A HIS* 3.3 4.3 + - - +
107A ALA* 3.0 20.5 + - - +
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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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20A LYS* 4.4 12.8 + - - +
24A LEU* 3.1 25.4 - - + +
98A PRO 4.3 2.3 + - - +
99A ASP* 2.8 26.1 + - - +
100A SER 3.1 15.3 + - - +
101A PRO* 3.5 10.1 - - - +
103A GLY* 1.3 72.7 - - - +
105A LEU* 1.3 49.5 + - - +
107A ALA* 3.1 8.8 - - - +
108A SER* 2.6 41.6 + - - +
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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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21A LEU* 4.3 16.8 - - + -
24A LEU* 3.0 40.4 - - + +
25A ALA* 4.1 10.1 - - + +
85A LEU* 3.0 32.1 - - + -
101A PRO 3.1 9.1 + - - +
102A VAL* 2.9 16.6 + - + +
103A GLY 2.8 1.2 + - - -
104A GLN* 1.3 73.2 - - - +
106A HIS* 1.3 66.5 + - - +
107A ALA 2.9 0.7 - - - -
108A SER* 2.8 4.4 + - - -
109A LEU* 2.8 25.8 + - + +
147A LEU* 3.8 25.8 - - + -
150A LEU* 4.0 10.8 - - + -
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Residues in contact with HIS 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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82A GLU* 2.7 39.9 + - - -
85A LEU* 3.5 22.8 - - + +
86A GLY* 3.3 36.0 - - - -
102A VAL* 3.1 7.1 + - + +
103A GLY* 4.0 6.5 - - - +
105A LEU* 1.3 78.7 - - - +
107A ALA* 1.3 72.0 + - - +
109A LEU* 3.2 4.4 + - - +
110A LEU* 3.2 31.4 + - + +
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Residues in contact with ALA 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 GLY 3.0 14.8 + - - +
104A GLN* 3.1 16.4 - - - +
106A HIS* 1.3 85.1 + - - +
108A SER* 1.3 63.5 + - - +
110A LEU* 3.5 4.6 - - - +
111A GLY* 3.1 16.1 + - - -
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Residues in contact with SER 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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17A LEU* 4.3 11.1 - - - +
20A LYS* 3.5 37.2 + - - +
21A LEU* 4.4 17.0 - - - +
24A LEU* 4.2 2.3 - - - +
104A GLN* 2.6 28.1 + - - +
105A LEU* 2.8 2.8 + - - -
107A ALA* 1.3 70.9 - - - +
109A LEU* 1.3 68.4 + - - +
111A GLY* 3.7 2.2 - - - +
112A LEU* 3.0 21.3 + - - +
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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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21A LEU* 3.5 25.1 - - + +
78A LEU* 3.7 25.6 - - + +
81A TYR* 3.4 14.8 - - + -
82A GLU* 2.9 41.1 - - + +
85A LEU* 3.6 19.3 - - + -
105A LEU* 2.8 16.9 + - + +
106A HIS 3.2 8.9 + - - +
108A SER* 1.3 67.5 - - - +
110A LEU* 1.3 69.8 + - - +
112A LEU* 2.8 9.0 + - - +
113A SER* 2.7 23.2 + - - -
150A LEU* 4.3 18.2 - - + -
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Residues in contact with LEU 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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79A ILE* 5.4 1.3 - - + -
82A GLU* 3.6 30.6 - - + +
106A HIS* 3.5 17.7 - - + +
107A ALA* 3.5 10.5 - - - +
109A LEU* 1.3 77.9 - - - +
111A GLY* 1.3 57.9 + - - +
113A SER* 2.6 34.2 + - - +
114A GLN* 2.7 43.6 + - + +
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Residues in contact with GLY 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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17A LEU* 5.2 8.3 - - - -
107A ALA 3.1 10.9 + - - -
108A SER* 3.7 5.4 - - - -
109A LEU 3.2 0.2 + - - -
110A LEU* 1.3 79.5 - - - +
112A LEU* 1.3 57.5 + - - +
114A GLN* 3.1 11.4 - - - +
115A LEU* 2.9 25.6 + - - +
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Residues in contact with LEU 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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14A CYS* 3.8 41.3 - - + -
17A LEU* 4.2 17.1 - - + +
18A SER* 4.1 10.8 - - - -
21A LEU* 3.4 28.5 - - + -
74A ILE* 5.4 0.2 - - + -
78A LEU* 3.7 21.1 - - + -
108A SER 3.0 11.2 + - - +
109A LEU 2.8 10.6 + - - +
111A GLY* 1.3 69.8 - - - -
113A SER* 1.3 69.1 + - - +
115A LEU* 3.1 14.6 + - + +
116A LEU* 3.2 14.5 + - + +
157A ALA* 5.5 2.2 - - + -
161A PHE* 4.1 21.8 - - + -
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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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75A HIS* 3.2 12.5 + - - -
78A LEU* 3.3 26.4 + - - +
79A ILE* 2.8 36.2 - - - +
82A GLU* 4.4 0.7 - - - +
109A LEU 2.7 11.9 + - - -
110A LEU* 2.6 23.3 + - - -
112A LEU* 1.3 68.7 - - - +
114A GLN* 1.3 60.3 + - - -
116A LEU* 2.7 24.0 + - - +
117A GLN 2.9 11.8 + - - -
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Residues in contact with GLN 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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75A HIS* 5.0 0.4 - - - -
79A ILE* 5.0 2.8 - - - +
110A LEU* 2.7 41.5 + - + +
111A GLY* 3.1 11.9 - - - +
113A SER* 1.3 80.0 - - - +
115A LEU* 1.3 62.5 + - - +
116A LEU 3.0 1.0 + - - -
117A GLN 3.7 11.5 + - - -
118A PRO* 3.0 32.6 - - + +
119A GLU* 4.0 25.0 + - - +
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Residues in contact with LEU 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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9A PRO* 4.7 6.1 - - - +
10A ALA* 4.2 20.6 - - + +
13A GLN* 3.6 23.3 - - + +
14A CYS* 3.5 24.7 - - - -
17A LEU* 3.2 34.8 - - + -
111A GLY 2.9 12.1 + - - +
112A LEU* 3.5 14.4 - - + +
113A SER 3.1 0.6 - - - -
114A GLN* 1.3 75.7 - - - +
116A LEU* 1.3 60.7 + - - +
118A PRO* 4.6 3.2 - - - +
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Residues in contact with LEU 116 (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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9A PRO* 4.6 9.4 - - + -
14A CYS* 4.5 6.1 - - - -
71A LEU* 4.3 17.9 - - + +
74A ILE* 3.5 17.7 - - + -
75A HIS* 3.9 19.3 - - + +
78A LEU* 3.4 32.8 - - + -
112A LEU* 3.3 10.8 - - + +
113A SER 2.7 7.3 + - - +
115A LEU* 1.3 85.1 - - - +
117A GLN* 1.3 69.5 + - - +
118A PRO* 3.5 5.3 - - - +
161A PHE* 3.8 29.2 - - + -
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Residues in contact with GLN 117 (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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72A GLN* 6.2 4.0 - - + -
75A HIS* 2.9 46.0 - - + +
113A SER 2.9 8.4 + - - +
114A GLN* 3.4 6.0 + - - -
116A LEU* 1.3 83.2 + - - +
118A PRO* 1.3 57.2 - - - +
119A GLU* 2.3 23.1 + - - -
120A GLY* 4.1 10.7 - - - +
121A HIS* 3.0 37.1 + - - -
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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