Contacts of the helix formed by residues 75 - 88 (chain A) in PDB entry 2YG9
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 75 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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74A LEU* 1.3 77.4 - - - +
76A VAL* 1.3 58.7 + - - +
77A LYS* 3.8 5.4 + - - +
78A ALA* 3.1 26.4 + - - +
79A ALA* 2.9 27.9 + - - +
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Residues in contact with VAL 76 (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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74A LEU 4.7 1.1 - - - +
75A SER* 1.3 73.7 - - - +
77A LYS* 1.3 62.9 + - + +
79A ALA* 3.5 6.0 + - - +
80A GLN* 3.2 22.3 + - - +
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Residues in contact with LYS 77 (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 SER* 3.3 5.6 + - - +
76A VAL* 1.3 76.6 - - + +
78A ALA* 1.3 59.8 + - - +
80A GLN* 3.3 6.5 + - - +
81A ALA* 3.0 27.9 + - - +
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Residues in contact with ALA 78 (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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74A LEU* 4.0 13.8 - - + +
75A SER* 3.1 29.8 + - - +
77A LYS* 1.3 73.4 - - - +
79A ALA* 1.3 65.9 + - - +
81A ALA* 3.5 6.7 + - - +
82A ILE* 3.1 27.0 + - - +
85A ARG* 5.0 1.0 + - - -
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Residues in contact with ALA 79 (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 ARG* 5.5 4.9 - - + +
70A ALA* 5.6 0.2 - - - +
71A GLY* 3.6 28.8 + - - +
74A LEU* 4.0 5.5 - - + +
75A SER 2.9 17.9 + - - +
76A VAL* 3.7 7.4 - - - +
78A ALA* 1.3 76.0 - - - +
80A GLN* 1.3 62.8 + - - +
82A ILE* 3.2 23.5 - - - +
83A TYR* 3.2 12.0 + - - +
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Residues in contact with GLN 80 (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 ARG* 2.9 32.6 + - - +
76A VAL* 3.2 14.4 + - + +
77A LYS* 3.7 9.0 - - - +
78A ALA 3.3 0.4 - - - -
79A ALA* 1.3 76.4 - - - +
81A ALA* 1.3 57.6 + - - +
83A TYR* 3.3 4.4 + - - +
84A GLY* 3.0 29.4 + - - +
87A GLU* 4.5 7.5 + - - -
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Residues in contact with ALA 81 (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 LYS 3.0 16.7 + - - +
78A ALA* 3.6 8.7 - - - +
79A ALA 3.4 0.2 - - - -
80A GLN* 1.3 76.9 - - - +
82A ILE* 1.3 57.3 + - - +
84A GLY* 3.2 4.0 + - - -
85A ARG* 3.0 49.2 + - - +
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Residues in contact with ILE 82 (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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70A ALA* 4.0 17.5 - - + +
74A LEU* 4.0 19.7 - - + -
78A ALA 3.1 13.7 + - - +
79A ALA* 3.2 18.4 - - - +
81A ALA* 1.3 75.5 - - - +
83A TYR* 1.3 68.7 + - - +
85A ARG* 3.2 17.9 + - - +
86A LEU* 3.0 23.2 + - + +
109A VAL* 3.6 20.2 - - + +
110A GLY* 3.5 34.8 - - - +
111A LEU* 3.6 23.3 - - + +
115A LYS* 5.7 0.7 - - - +
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Residues in contact with TYR 83 (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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60A ASP* 4.7 3.5 + - - -
63A GLY* 3.3 38.7 + - - -
66A VAL* 4.1 6.1 - - + -
67A ARG* 3.4 68.6 - - + +
70A ALA* 5.1 2.0 - - + -
79A ALA 3.2 14.1 + - - +
80A GLN* 3.3 5.6 + - - +
82A ILE* 1.3 84.2 - - + +
84A GLY* 1.3 55.8 + - - +
86A LEU* 3.2 16.6 + - + +
87A GLU* 2.9 52.8 + - - +
93A VAL* 3.7 25.9 - - + +
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Residues in contact with GLY 84 (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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80A GLN* 3.0 18.5 + - - +
81A ALA* 3.2 5.1 + - - -
83A TYR* 1.3 77.2 - - - +
85A ARG* 1.3 60.6 + - - +
87A GLU* 3.4 18.8 + - - +
88A GLY* 3.1 17.5 + - - -
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Residues in contact with ARG 85 (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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78A ALA 5.0 1.0 + - - -
81A ALA* 3.0 35.4 + - - +
82A ILE* 3.2 30.1 + - - +
84A GLY* 1.3 74.2 - - - +
86A LEU* 1.3 63.7 + - - +
88A GLY* 3.2 10.9 + - - +
89A LEU* 3.3 16.5 + - - +
108A GLY 5.4 0.4 + - - -
109A VAL* 2.8 50.9 + - + +
110A GLY* 4.7 2.2 - - - -
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Residues in contact with LEU 86 (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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66A VAL* 3.8 26.9 - - + -
70A ALA* 4.0 20.9 - - + -
82A ILE 3.0 17.9 + - - +
83A TYR* 3.4 11.9 - - + +
85A ARG* 1.3 76.6 - - - +
87A GLU* 1.3 60.9 + - - +
88A GLY 3.0 0.2 - - - -
89A LEU* 3.0 39.5 + - + +
92A GLY* 4.1 6.1 - - - +
93A VAL* 3.8 18.2 - - + +
98A LEU* 4.9 6.6 - - + +
106A LEU* 3.9 13.0 - - + -
109A VAL* 3.7 25.4 - - + -
111A LEU* 4.2 13.2 - - + -
119A VAL* 5.5 2.5 - - + -
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Residues in contact with GLU 87 (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 ARG* 4.8 3.6 + - - -
80A GLN* 4.5 5.7 + - - -
83A TYR* 2.9 43.4 + - + +
84A GLY* 3.4 22.9 + - - +
86A LEU* 1.3 74.9 - - - +
88A GLY* 1.3 59.4 + - - +
89A LEU 3.3 6.5 - - - +
92A GLY* 3.7 11.9 + - - -
93A VAL* 3.6 13.4 - - + +
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Residues in contact with GLY 88 (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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84A GLY 3.1 12.4 + - - -
85A ARG* 3.2 7.6 + - - -
86A LEU 3.0 1.2 - - - -
87A GLU* 1.3 73.6 - - - +
89A LEU* 1.3 66.4 + - - +
90A PRO* 3.7 1.9 - - - +
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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