Contacts of the helix formed by residues 93 - 108 (chain A) in PDB entry 2YYU
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 GLY 93 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90A ALA 3.0 12.9 + - - -
91A ALA 3.1 1.8 - - - -
92A GLY* 1.3 80.2 - - - +
94A ARG* 1.3 65.9 + - - -
95A ARG 3.4 2.7 - - - -
96A MET 3.4 2.3 + - - -
97A MET* 3.0 28.5 + - - +
151A LEU* 5.8 1.8 - - - -
130B MET* 4.1 11.9 - - - -
134B GLU* 3.0 14.8 - - - -
135B LEU* 4.9 2.2 - - - -
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Residues in contact with ARG 94 (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 GLY* 1.3 68.1 - - - -
95A ARG* 1.3 60.7 + - - +
97A MET* 3.2 1.7 + - - -
98A GLU* 2.9 42.8 + - - +
147A HIS* 5.4 4.0 - - - -
151A LEU* 3.1 35.3 - - + +
154A GLU* 2.8 38.2 + - - +
155A SER* 3.3 21.6 + - - +
130B MET* 5.4 0.2 - - - -
133B GLU 5.6 1.8 + - - -
134B GLU* 2.7 34.2 + - - +
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Residues in contact with ARG 95 (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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68A PRO* 3.3 36.4 - - + +
93A GLY* 3.4 0.6 - - - -
94A ARG* 1.3 77.9 - - - +
96A MET* 1.3 58.9 + - - +
98A GLU* 3.3 16.8 + - - +
99A ALA* 2.9 29.2 + - - +
125B SER* 4.1 18.6 + - - +
130B MET* 6.2 3.3 - - - -
134B GLU* 5.2 1.2 + - - -
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Residues in contact with MET 96 (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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64A LEU 4.0 12.3 - - - +
65A HIS* 4.1 2.5 - - - -
66A ASP 3.1 40.6 - - - +
68A PRO* 4.0 20.9 - - + +
71A VAL* 3.6 18.6 - - + +
88A VAL* 4.0 15.9 - - + -
89A HIS 3.3 26.0 - - - +
92A GLY* 3.5 31.3 + - - +
93A GLY 3.4 1.8 + - - +
94A ARG 3.3 0.4 - - - -
95A ARG* 1.3 78.8 - - - +
97A MET* 1.3 70.4 + - + +
99A ALA* 3.1 3.8 + - - +
100A ALA* 2.9 26.7 + - - +
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Residues in contact with MET 97 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88A VAL* 3.3 12.6 - - + -
89A HIS 4.5 1.3 - - - +
90A ALA* 3.4 25.8 - - + +
93A GLY 3.0 17.2 + - - +
94A ARG* 3.2 2.0 + - - +
96A MET* 1.3 86.9 - - + +
98A GLU* 1.3 62.5 + - - +
100A ALA* 3.3 16.4 + - - +
101A ILE* 3.4 17.5 + - - +
119A ALA* 2.9 37.9 - - + -
151A LEU* 4.4 2.9 - - - +
152A ALA* 3.8 22.0 - - + -
155A SER* 3.6 19.3 - - - -
157A LEU* 3.3 23.6 - - + +
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Residues in contact with GLU 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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94A ARG* 2.9 27.6 + - - +
95A ARG* 3.6 24.3 + - - +
97A MET* 1.3 75.4 - - - +
99A ALA* 1.3 64.5 + - - +
101A ILE* 3.2 8.7 + - - +
102A GLU* 3.1 27.9 + - + +
154A GLU 4.8 3.1 - - - +
155A SER* 3.6 32.6 - - - +
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Residues in contact with ALA 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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68A PRO* 3.6 32.1 - - + +
72A LYS* 3.6 15.5 - - + +
95A ARG* 2.9 15.5 + - - +
96A MET 3.1 9.2 + - - +
98A GLU* 1.3 75.3 - - - +
100A ALA* 1.3 65.8 + - - +
102A GLU* 3.0 19.2 + - - +
103A GLY 2.8 19.8 + - - -
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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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71A VAL* 3.9 14.1 - - + +
75A MET* 3.5 26.9 - - + +
88A VAL* 4.2 16.6 - - + -
96A MET 2.9 12.5 + - - +
97A MET* 3.4 11.9 - - - +
98A GLU 3.2 0.2 - - - -
99A ALA* 1.3 76.6 - - - +
101A ILE* 1.3 63.5 + - - +
103A GLY 3.2 1.6 + - - -
104A LEU* 2.9 29.2 + - - +
117A CYS* 4.5 8.3 - - - -
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Residues in contact with ILE 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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97A MET 3.4 13.9 - - - +
98A GLU* 3.3 8.7 - - - +
99A ALA 3.1 0.2 - - - -
100A ALA* 1.3 76.9 - - - +
102A GLU* 1.3 63.8 + - + +
104A LEU* 3.3 6.5 + - + +
105A ASP* 3.1 34.1 + - - +
114A ARG* 3.9 29.8 - - - +
117A CYS* 4.2 17.3 - - + -
155A SER 4.3 7.4 - - - +
156A GLY* 3.9 18.2 - - - +
157A LEU* 3.8 22.4 - - + -
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Residues in contact with GLU 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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72A LYS* 3.0 38.4 + - - +
98A GLU* 3.1 20.2 - - - +
99A ALA* 3.0 13.7 + - - +
101A ILE* 1.3 76.9 - - + +
103A GLY* 1.3 64.6 + - - +
105A ASP* 3.2 9.6 + - - +
106A ALA* 3.0 24.1 + - - +
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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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72A LYS* 3.3 32.7 - - - +
75A MET* 4.1 0.4 - - - -
76A LYS* 3.0 19.2 - - - +
99A ALA 2.8 11.7 + - - -
100A ALA 3.6 3.4 - - - -
102A GLU* 1.3 77.7 - - - +
104A LEU* 1.3 61.2 + - - +
106A ALA* 3.3 4.6 + - - -
107A GLY 2.9 18.0 + - - -
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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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75A MET* 3.6 37.4 - - + +
78A LEU* 5.0 0.2 - - + -
79A ALA* 3.5 15.2 - - + +
86A VAL* 4.0 15.9 - - + -
100A ALA 2.9 22.6 + - - +
101A ILE* 3.7 7.2 - - - +
103A GLY* 1.3 74.6 - - - +
105A ASP* 1.3 63.1 + - - +
107A GLY 3.1 1.2 + - - -
108A THR* 2.8 30.2 + - - -
114A ARG* 4.2 16.4 - - + +
115A PRO* 3.5 30.1 - - + +
117A CYS* 3.7 28.3 - - + -
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Residues in contact with ASP 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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101A ILE* 3.1 30.0 + - - +
102A GLU* 3.2 11.1 + - - +
104A LEU* 1.3 77.4 - - - +
106A ALA* 1.3 62.1 + - - +
107A GLY 3.1 1.0 + - - -
108A THR* 3.1 21.0 + - - +
114A ARG* 3.6 24.2 + - - +
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Residues in contact with ALA 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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72A LYS* 5.5 3.4 - - - -
76A LYS* 3.6 35.4 - - + +
80A ARG* 5.4 1.4 + - - -
102A GLU 3.0 16.3 + - - +
103A GLY 3.8 0.4 - - - +
105A ASP* 1.3 77.1 - - - +
107A GLY* 1.3 58.1 + - - +
108A THR 3.5 3.0 - - - +
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Residues in contact with GLY 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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76A LYS* 3.5 26.2 - - - -
79A ALA* 3.6 9.9 - - - +
80A ARG* 3.1 27.3 + - - +
103A GLY 2.9 11.0 + - - -
104A LEU 3.6 4.9 - - - -
105A ASP 3.0 0.4 - - - -
106A ALA* 1.3 79.9 - - - +
108A THR* 1.3 60.6 + - - +
109A PRO* 3.9 4.3 - - - +
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Residues in contact with THR 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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79A ALA* 4.0 2.0 - - - +
104A LEU 2.8 18.4 + - - -
105A ASP* 3.1 13.8 + - - +
106A ALA 4.6 2.4 - - - +
107A GLY* 1.3 78.9 - - - +
109A PRO* 1.3 83.1 - - + +
110A SER* 4.4 2.7 - - - +
112A ARG* 3.3 32.3 - - + +
113A MET 3.8 11.9 - - - +
114A ARG* 3.1 20.8 - - - +
115A PRO* 3.3 9.5 - - + +
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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