Contacts of the helix formed by residues 106 - 124 (chain A) in PDB entry 2G2Y
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 ASP 106 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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104A VAL 4.3 0.6 + - - -
105A ILE* 1.3 75.2 - - - +
107A PHE* 1.3 63.0 + - - +
108A ALA* 3.0 13.6 + - - +
109A ASP* 2.8 48.1 + - - +
110A ALA* 2.9 25.6 + - - +
112A ARG* 4.5 0.7 + - - -
220A THR 4.8 3.4 + - - -
222A ASN* 5.2 4.9 - - - +
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Residues in contact with PHE 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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32A THR* 3.6 43.5 - - + -
35A GLU* 3.6 29.2 - - + -
36A ALA* 4.0 6.1 - - + -
67A LEU* 4.8 2.5 - - + -
68A THR* 4.0 15.5 - - + -
71A VAL* 3.9 30.1 - - + -
75A ARG* 3.7 20.4 - - - +
100A VAL* 4.1 19.4 - - + +
105A ILE 3.4 2.8 + - - -
106A ASP* 1.3 75.9 + - - +
108A ALA* 1.3 60.7 + - + +
110A ALA* 3.2 3.1 + - - +
111A VAL* 3.0 46.3 + - + +
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Residues in contact with ALA 108 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35A GLU* 5.4 5.8 - - + +
36A ALA* 6.1 0.7 - - - +
39A ALA* 4.3 9.9 - - + +
106A ASP* 3.0 11.7 + - - +
107A PHE* 1.3 81.7 - - + +
109A ASP* 1.3 66.1 + - - +
111A VAL* 3.3 8.5 + - - +
112A ARG* 3.2 48.6 + - - +
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Residues in contact with ASP 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 ILE* 4.1 2.7 - - + -
106A ASP* 2.8 35.3 + - + +
108A ALA* 1.3 75.7 - - - +
110A ALA* 1.3 56.5 + - - +
112A ARG* 3.0 28.0 + - - +
113A LEU* 2.8 30.8 + - - +
219A ILE* 3.9 45.3 - - + +
220A THR* 4.7 7.6 + - - +
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Residues in contact with ALA 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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67A LEU* 4.2 12.3 - - + -
96A TYR* 5.1 3.6 - - + +
100A VAL* 3.4 32.5 - - + -
105A ILE* 3.9 15.2 - - + +
106A ASP 2.9 9.2 + - - +
107A PHE 3.5 6.1 - - - +
109A ASP* 1.3 76.4 - - - +
111A VAL* 1.3 59.0 + - - +
113A LEU* 3.1 9.0 + - - +
114A VAL* 2.9 35.1 + - - +
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Residues in contact with VAL 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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36A ALA* 4.0 15.0 - - + +
39A ALA* 4.4 6.5 - - + -
40A LEU* 3.5 36.1 - - + -
64A PRO* 4.1 8.1 - - + +
67A LEU* 5.2 5.6 - - + -
68A THR* 3.9 12.6 - - - +
107A PHE* 3.0 44.4 + - + +
108A ALA* 3.6 9.6 - - - +
109A ASP 3.2 0.4 - - - -
110A ALA* 1.3 76.7 - - - +
112A ARG* 1.3 63.4 + - - +
114A VAL* 3.5 9.3 - - - +
115A GLU* 3.2 21.1 + - - +
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Residues in contact with ARG 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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39A ALA* 3.5 46.2 - - + +
40A LEU* 4.9 2.9 - - + -
106A ASP* 4.5 0.8 + - - -
108A ALA* 3.2 20.6 + - - +
109A ASP* 3.0 39.5 + - - +
111A VAL* 1.3 80.4 - - + +
113A LEU* 1.3 63.1 - - - +
115A GLU* 3.3 12.3 + - - +
116A MET* 3.1 34.3 + - + +
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Residues in contact with LEU 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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96A TYR* 4.5 16.4 - - + -
105A ILE* 4.9 9.6 - - + -
109A ASP 2.8 16.5 + - - +
110A ALA* 3.1 12.3 + - - +
112A ARG* 1.3 78.3 - - - +
114A VAL* 1.3 60.0 + - + +
116A MET* 3.0 15.4 + - + +
117A ARG* 2.8 26.0 + - - +
212A LEU* 4.4 9.2 - - + -
215A GLU* 4.0 29.8 - - + +
216A LEU* 3.3 33.2 - - + -
219A ILE* 4.3 23.6 - - + -
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Residues in contact with VAL 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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63A GLN* 3.4 24.4 - - + +
64A PRO* 3.5 28.7 - - + -
67A LEU* 4.1 6.7 - - + -
93A LEU* 3.7 14.1 - - + -
96A TYR* 3.7 40.6 - - + -
110A ALA 2.9 22.9 + - - +
111A VAL* 3.5 9.4 - - - +
113A LEU* 1.3 72.6 - - - +
115A GLU* 1.3 62.6 + - - +
117A ARG* 3.7 7.6 - - - -
118A GLY* 2.8 26.0 + - - -
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Residues in contact with GLU 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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39A ALA 5.5 0.3 - - - +
40A LEU* 3.5 35.0 - - + +
42A TYR* 3.9 17.2 + - - -
60A TRP* 3.6 26.1 - - + +
64A PRO* 4.4 1.8 - - + -
111A VAL 3.2 14.2 + - - +
112A ARG* 3.4 14.1 - - - +
114A VAL* 1.3 78.5 - - - +
116A MET* 1.3 64.6 + - + +
118A GLY* 3.2 2.8 + - - -
119A LYS* 3.0 50.8 + - + +
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Residues in contact with MET 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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112A ARG* 3.1 27.2 + - + +
113A LEU* 3.0 22.2 + - + +
115A GLU* 1.3 76.3 - - + +
117A ARG* 1.3 67.3 - - - +
119A LYS* 2.9 14.6 + - + +
120A PHE* 2.8 45.0 + - + -
215A GLU* 3.5 40.4 - - + +
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Residues in contact with ARG 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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63A GLN* 2.8 28.5 + - - -
92A SER 4.2 3.8 - - - -
93A LEU* 4.3 5.3 - - - +
96A TYR* 3.2 43.7 + - - -
113A LEU 2.8 17.0 + - - +
114A VAL* 3.4 12.8 - - - +
116A MET* 1.3 71.6 - - - +
118A GLY* 1.3 57.3 + - - +
120A PHE* 3.2 11.7 + - - +
121A MET* 2.9 42.9 + - - +
201A HIS* 4.1 1.4 - - - -
212A LEU* 4.0 15.1 - - + +
250A GLN* 2.9 25.5 + - - -
251A LEU* 3.6 25.0 - - + +
1001A MLI 2.5 44.2 + - - -
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Residues in contact with GLY 118 (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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59A THR* 3.6 6.6 - - - +
60A TRP* 3.8 19.1 - - - -
63A GLN* 3.3 21.7 - - - +
114A VAL 2.8 16.9 + - - -
115A GLU 3.6 3.8 - - - -
116A MET 3.2 0.4 - - - -
117A ARG* 1.3 73.7 - - - +
119A LYS* 1.3 56.0 + - - +
121A MET* 3.3 1.1 + - - +
122A GLN* 3.0 30.1 + - - +
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Residues in contact with LYS 119 (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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60A TRP* 3.6 33.4 - - + +
115A GLU* 3.0 38.8 + - + +
116A MET* 2.9 15.7 + - + +
118A GLY* 1.3 74.3 - - - +
120A PHE* 1.3 69.7 + - + +
122A GLN* 3.3 5.9 + - - +
123A GLU* 3.2 29.6 + - - +
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Residues in contact with PHE 120 (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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116A MET* 2.8 40.5 + - + -
117A ARG* 3.6 10.3 - - - +
119A LYS* 1.3 76.7 - - + +
121A MET* 1.3 64.0 + - + +
123A GLU* 3.2 21.6 - - - +
124A ALA* 3.2 16.5 + - - -
208A ALA* 3.6 28.2 - - + +
211A LYS* 3.7 45.1 - - + -
212A LEU* 3.7 22.7 - - + -
215A GLU* 3.8 28.9 - - + -
251A LEU* 5.8 0.9 - - + -
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Residues in contact with MET 121 (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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11A GLN* 5.4 0.2 - - - +
59A THR* 4.8 6.3 - - + +
63A GLN* 3.5 23.6 - - - +
117A ARG* 2.9 31.7 + - - +
118A GLY 3.7 4.0 - - - +
120A PHE* 1.3 78.1 - - - +
122A GLN* 1.3 63.2 + - - +
124A ALA* 3.0 19.2 + - - +
125A VAL 4.5 0.3 + - - -
198A VAL* 3.9 26.1 - - + +
199A PRO* 5.7 0.5 - - - +
200A SER* 3.8 22.7 - - - -
205A MET* 3.6 23.8 - - + -
251A LEU* 3.7 20.9 - - + -
1001A MLI 3.6 27.8 - - + +
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Residues in contact with GLN 122 (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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58A LYS* 5.5 0.2 - - - -
59A THR* 3.3 22.9 + - - +
60A TRP* 3.4 30.3 - - + -
118A GLY 3.0 17.2 + - - +
119A LYS* 3.3 6.0 + - - +
121A MET* 1.3 76.6 - - - +
123A GLU* 1.3 60.3 + - + +
125A VAL 3.6 13.0 - - - +
127A GLU* 4.3 24.3 + - - +
197A SER* 4.3 5.7 + - - -
198A VAL* 3.9 20.7 - - - +
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Residues in contact with GLU 123 (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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119A LYS* 3.2 15.5 + - - +
120A PHE* 3.2 32.5 - - - +
122A GLN* 1.3 77.1 - - + +
124A ALA* 1.3 66.7 + - - +
125A VAL* 3.0 8.6 + - - -
211A LYS* 4.1 18.2 - - - +
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Residues in contact with ALA 124 (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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120A PHE 3.2 11.3 + - - +
121A MET 3.0 17.3 + - - +
123A GLU* 1.3 80.6 - - - +
125A VAL* 1.3 66.5 + - + +
126A PRO* 4.7 0.7 - - - +
199A PRO* 5.8 3.1 - - + -
204A LEU* 4.1 14.5 - - + +
205A MET* 3.8 24.7 - - + -
207A PRO* 6.0 5.6 - - + +
208A ALA* 4.4 6.3 - - + +
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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