Contacts of the helix formed by residues 9 - 21 (chain A) in PDB entry 2YGE
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 GLN 9 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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7A GLU 3.7 2.2 + - - -
8A PHE* 1.3 71.5 - - - +
10A ALA* 1.3 78.2 + - - +
11A GLU* 3.9 12.3 - - - +
12A ILE* 3.0 17.2 + - + +
13A THR* 3.2 7.8 + - - -
94A GLY 2.9 20.2 + - - +
95A THR* 3.8 15.6 - - - +
96A ILE* 4.7 0.7 - - - -
97A ALA* 3.5 40.9 + - + +
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Residues in contact with ALA 10 (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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8A PHE 3.4 4.6 + - - -
9A GLN* 1.3 83.3 - - - +
11A GLU* 1.3 61.7 + - + +
13A THR* 3.5 8.1 + - - -
14A GLN* 2.9 39.8 + - - +
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Residues in contact with GLU 11 (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 GLN* 3.2 9.5 - - + +
10A ALA* 1.3 73.9 - - + +
12A ILE* 1.3 62.2 + - - +
14A GLN* 3.1 31.9 + - - +
15A LEU* 2.9 28.2 + - - +
97A ALA* 4.1 20.6 - - + -
101A THR* 3.6 21.3 - - + +
102A LYS* 3.4 33.0 + - + +
105A MET* 3.6 10.7 - - - +
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Residues in contact with ILE 12 (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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8A PHE* 3.6 19.3 - - + -
9A GLN* 3.0 9.0 + - + +
11A GLU* 1.3 76.9 - - - +
13A THR* 1.3 57.1 + - - +
15A LEU* 3.2 8.1 + - + +
16A MET* 2.9 30.7 + - + +
94A GLY* 3.2 36.1 - - - +
96A ILE 4.0 3.8 - - - +
97A ALA* 3.9 28.7 - - + +
98A ASN* 4.3 6.1 - - - +
101A THR* 4.4 9.6 - - + +
125A TYR* 3.5 40.2 - - + +
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Residues in contact with THR 13 (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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8A PHE* 3.1 28.6 + - - +
9A GLN 3.2 4.8 + - - -
10A ALA* 3.6 10.9 - - - -
12A ILE* 1.3 79.2 - - - +
14A GLN* 1.3 63.3 + - + +
16A MET* 3.4 11.6 + - + +
17A SER* 3.0 22.0 + - - -
152A ALA 5.1 3.6 - - - +
153A GLY 4.7 3.6 - - - +
154A GLY* 4.1 20.9 - - - +
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Residues in contact with GLN 14 (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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10A ALA* 2.9 31.0 + - - +
11A GLU* 3.1 33.0 + - - +
13A THR* 1.3 75.2 - - + +
15A LEU* 1.3 60.2 + - - +
17A SER* 3.0 9.0 + - - -
18A LEU* 2.9 30.4 + - + +
105A MET* 3.7 17.7 - - - +
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Residues in contact with LEU 15 (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 GLU 2.9 13.2 + - - +
12A ILE* 3.5 10.5 - - + +
14A GLN* 1.3 76.2 - - - +
16A MET* 1.3 62.1 + - - +
18A LEU* 3.2 7.1 + - + +
19A ILE* 3.0 45.5 + - + +
101A THR* 4.0 17.9 - - + +
104A PHE* 3.6 29.6 - - + -
105A MET* 3.5 21.9 - - + -
122A VAL* 4.0 19.3 - - + -
125A TYR* 4.0 33.2 - - + -
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Residues in contact with MET 16 (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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8A PHE* 3.5 36.6 - - + -
12A ILE 2.9 14.7 + - - +
13A THR* 3.8 13.7 - - - +
15A LEU* 1.3 75.0 - - - +
17A SER* 1.3 57.1 + - - +
19A ILE* 3.9 5.3 - - - +
20A ILE* 2.8 36.2 + - - +
125A TYR* 3.7 26.5 - - + -
128A PHE* 3.6 34.2 - - + +
148A TRP* 5.9 0.2 - - - -
152A ALA* 3.6 21.8 - - + +
153A GLY 3.2 27.1 - - - +
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Residues in contact with SER 17 (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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13A THR* 3.0 14.2 + - - -
14A GLN* 3.0 13.8 + - - -
16A MET* 1.3 74.2 - - - +
18A LEU* 1.3 69.2 + - - +
20A ILE* 4.8 2.2 - - - -
21A ASN* 3.0 41.1 + - - +
152A ALA* 5.4 1.7 + - - -
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Residues in contact with LEU 18 (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 GLN 2.9 14.4 + - - +
15A LEU* 3.4 7.9 - - + +
17A SER* 1.3 75.0 - - - +
19A ILE* 1.3 66.4 + - + +
21A ASN* 3.2 20.6 - - - +
22A THR* 3.5 5.5 + - - -
105A MET* 3.4 45.5 - - + +
108A LEU* 4.1 24.9 - - + -
109A SER* 6.6 0.2 - - - -
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Residues in contact with ILE 19 (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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15A LEU* 3.0 41.8 + - + +
16A MET* 3.9 2.9 - - - +
18A LEU* 1.3 77.6 - - + +
20A ILE* 1.3 62.9 + - - +
22A THR* 3.2 24.5 - - - +
104A PHE* 4.7 4.9 - - + -
108A LEU* 5.3 4.5 - - + -
114A VAL* 5.5 5.4 - - + -
117A ILE* 3.7 24.5 - - + -
125A TYR* 3.5 31.0 - - + +
126A SER* 4.5 1.1 - - - -
128A PHE* 3.9 6.3 - - + +
129A LEU* 3.6 36.9 - - + +
178A LYS* 4.9 0.3 + - - -
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Residues in contact with ILE 20 (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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16A MET 2.8 19.7 + - - +
17A SER* 4.9 1.3 - - - -
19A ILE* 1.3 74.1 - - - +
21A ASN* 1.3 82.9 + - - +
22A THR* 3.5 4.0 + - - +
128A PHE* 3.7 32.5 - - + +
131A ALA 4.0 7.2 - - - +
132A ASP* 4.2 13.9 - - + -
152A ALA* 4.0 16.8 - - + -
178A LYS* 3.3 43.8 + - - +
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Residues in contact with ASN 21 (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 SER* 3.0 37.3 + - - +
18A LEU* 3.2 9.5 - - - +
20A ILE* 1.3 91.7 - - - +
22A THR* 1.3 57.6 + - - +
23A VAL* 5.9 0.3 - - - +
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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