Contacts of the helix formed by residues 147 - 163 (chain A) in PDB entry 1YDY
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 THR 147 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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73A ASN* 5.0 6.3 - - + +
74A LEU 3.3 13.9 - - - +
75A VAL* 4.1 0.7 - - + +
76A VAL* 3.9 2.0 - - - -
109A LEU* 3.8 40.6 - - + -
113A LYS* 4.6 0.4 - - - -
146A HIS* 1.3 81.1 + - - +
148A PHE* 1.3 66.2 + - - +
149A GLU* 3.5 14.4 + - - +
150A GLU* 2.8 47.8 + - - +
151A GLU* 3.0 18.2 + - - +
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Residues in contact with PHE 148 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64A GLN* 4.0 17.7 - - + -
66A LEU* 3.7 36.8 - - + -
74A LEU* 3.0 27.4 + - + -
76A VAL* 4.0 7.5 - - - +
147A THR* 1.3 72.9 - - - +
149A GLU* 1.3 67.9 + - - +
151A GLU* 3.1 2.5 + - + -
152A ILE* 2.9 41.7 + - + +
168A ILE* 4.4 0.7 - - + -
170A PRO* 3.7 30.7 - - + -
189A THR* 4.2 5.4 - - + -
192A VAL* 3.5 27.6 - - + -
193A LEU* 3.8 29.4 - - + -
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Residues in contact with GLU 149 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73A ASN* 5.2 6.6 - - - +
74A LEU* 3.9 9.9 + - - +
147A THR* 3.7 13.6 - - - +
148A PHE* 1.3 90.0 + - - +
150A GLU* 1.3 58.2 + - + +
152A ILE* 3.2 3.6 + - - +
153A GLU* 2.9 38.1 + - - +
188A LYS* 4.6 11.3 + - - -
192A VAL* 3.7 35.1 - - + +
195A LYS* 4.9 9.7 + - + +
196A TYR* 3.8 27.5 + - + +
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Residues in contact with GLU 150 (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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48A LEU* 5.3 1.6 - - + -
113A LYS* 2.4 35.1 + - - -
146A HIS* 3.2 16.5 - - + +
147A THR* 2.8 46.4 + - - +
149A GLU* 1.3 76.4 - - + +
151A GLU* 1.3 57.2 - - - +
153A GLU* 3.5 2.2 + - - +
154A PHE* 3.0 13.5 + - - +
141B SER* 2.8 40.0 + - - +
142B ASP* 3.6 24.3 - - + +
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Residues in contact with GLU 151 (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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48A LEU* 4.5 6.3 - - + -
51A LYS* 2.8 43.4 + - + +
62A LEU* 4.5 1.4 - - - +
64A GLN* 2.8 37.7 + - + +
76A VAL* 3.6 11.9 - - + +
146A HIS* 2.8 34.2 + - + +
147A THR 3.0 7.5 + - - +
148A PHE* 3.7 6.7 - - + +
150A GLU* 1.3 76.1 - - - +
152A ILE* 1.3 66.9 + - - +
154A PHE* 3.1 7.4 + - + +
155A VAL* 2.9 28.4 + - + +
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Residues in contact with ILE 152 (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 GLN* 5.1 1.6 - - - -
148A PHE* 2.9 44.4 + - + +
149A GLU* 3.2 6.9 + - - +
151A GLU* 1.3 76.1 - - - +
153A GLU* 1.3 57.8 + - - +
155A VAL* 3.2 3.5 + - - +
156A GLN* 2.8 46.6 + - + +
168A ILE* 3.2 44.2 - - + -
192A VAL* 5.0 1.1 - - + -
193A LEU* 5.7 0.9 - - + -
196A TYR* 3.7 39.9 - - + -
198A TYR* 3.8 6.1 - - + +
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Residues in contact with GLU 153 (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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149A GLU* 2.9 21.1 + - - +
150A GLU* 3.8 3.9 - - - +
152A ILE* 1.3 76.9 - - - +
154A PHE* 1.3 53.3 + - - +
156A GLN* 4.3 4.8 - - - +
157A GLY* 2.8 32.6 + - - +
196A TYR* 2.6 37.7 + - + -
136B PHE* 3.8 3.6 - - - -
137B PRO* 5.3 0.2 - - - +
139B GLY 5.0 0.7 - - - +
140B LYS* 3.7 32.0 + - + +
141B SER* 2.8 35.3 + - - +
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Residues in contact with PHE 154 (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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48A LEU* 3.6 40.2 - - + -
51A LYS* 3.8 13.0 - - + -
52A ALA* 3.7 25.1 - - + -
62A LEU* 4.9 2.9 - - + -
150A GLU 3.0 15.9 + - - +
151A GLU* 3.2 12.8 - - + +
153A GLU* 1.3 76.8 - - - +
155A VAL* 1.3 73.9 + - + +
158A LEU* 3.0 48.0 + - + +
43B LEU* 3.6 20.4 - - + -
49B PRO* 3.9 14.6 - - + -
136B PHE* 3.6 9.6 - + - -
141B SER* 3.6 6.7 + - - +
143B PHE* 4.0 18.6 - + - -
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Residues in contact with VAL 155 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55A TYR* 4.6 3.6 - - + -
62A LEU* 3.8 27.1 - - + -
151A GLU* 2.9 27.4 + - + +
152A ILE 3.8 2.9 - - - +
154A PHE* 1.3 83.6 - - + +
156A GLN* 1.3 57.7 + - + +
158A LEU* 3.2 6.1 + - - +
159A ASN* 2.9 33.3 + - - +
166A ILE* 3.4 35.7 - - + +
167A GLY 4.6 1.6 - - - +
168A ILE* 4.2 26.5 - - + -
198A TYR* 5.2 3.1 - - - +
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Residues in contact with GLN 156 (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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152A ILE* 2.8 28.7 + - - +
153A GLU* 4.3 4.3 - - - +
155A VAL* 1.3 73.2 - - + +
157A GLY* 1.3 63.1 + - - +
159A ASN* 3.2 14.2 + - - +
160A HIS* 3.0 21.8 + - - +
196A TYR* 3.0 42.3 + - - +
198A TYR* 3.1 32.9 + - - +
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Residues in contact with GLY 157 (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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153A GLU 2.8 23.4 + - - -
155A VAL 3.2 0.2 - - - -
156A GLN* 1.3 74.6 - - - +
158A LEU* 1.3 56.1 + - - +
160A HIS* 3.2 6.0 + - - +
161A SER* 2.9 26.9 + - - -
136B PHE* 3.4 18.4 - - - -
137B PRO* 3.5 24.4 - - - +
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Residues in contact with LEU 158 (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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55A TYR* 3.3 39.9 - - + -
154A PHE* 3.0 50.6 + - + +
155A VAL 3.7 0.2 - - - +
157A GLY* 1.3 71.6 - - - +
159A ASN* 1.3 61.6 + - - +
160A HIS 3.0 1.8 - - - -
161A SER* 3.5 5.2 - - - +
162A THR* 2.7 43.9 + - + +
42B TYR* 3.6 22.4 - - + +
43B LEU* 3.7 20.2 - - + -
53B MET* 3.8 20.0 - - + -
136B PHE* 3.7 0.2 - - - -
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Residues in contact with ASN 159 (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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55A TYR* 2.6 29.0 + - - -
155A VAL* 2.9 22.2 + - - +
156A GLN* 3.2 15.8 + - - +
158A LEU* 1.3 76.7 - - - +
160A HIS* 1.3 58.0 + - - +
163A GLY* 2.9 27.9 + - - -
164A LYS 3.0 19.5 - - - +
165A ASN* 3.8 10.2 + - - +
166A ILE 2.9 39.9 + - - +
198A TYR* 5.5 1.6 + - - -
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Residues in contact with HIS 160 (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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156A GLN 3.0 12.5 + - - +
157A GLY* 3.3 11.2 - - - +
158A LEU 3.0 0.2 - - - -
159A ASN* 1.3 81.5 - - - +
161A SER* 1.3 63.8 + - - +
162A THR 3.4 0.2 + - - -
163A GLY* 3.7 5.2 + - - -
133B PRO 3.0 25.5 + - - -
134B GLY* 3.7 12.1 + - - +
135B ARG 3.2 21.1 + - - -
137B PRO* 4.4 11.7 - - + -
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Residues in contact with SER 161 (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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157A GLY 2.9 10.5 + - - -
158A LEU* 3.5 16.5 + - - +
160A HIS* 1.3 77.9 - - - +
162A THR* 1.3 60.5 + - - +
41B GLY 4.5 1.7 - - - +
42B TYR* 2.7 48.8 + - - +
134B GLY 3.4 15.8 - - - +
135B ARG* 3.7 4.0 - - - -
136B PHE 3.6 21.3 - - - -
347B PHE* 5.9 0.5 - - - -
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Residues in contact with THR 162 (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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55A TYR* 3.0 29.1 + - + -
158A LEU* 2.7 34.5 + - + +
161A SER* 1.3 78.9 - - - +
163A GLY* 1.3 57.5 + - - +
164A LYS* 3.1 27.6 + - + +
42B TYR* 3.7 33.4 - - + -
53B MET* 5.1 2.7 - - + -
57B GLN* 6.2 0.4 - - - +
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Residues in contact with GLY 163 (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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159A ASN 2.9 12.6 + - - -
160A HIS 3.7 5.1 + - - -
161A SER 3.6 1.6 - - - -
162A THR* 1.3 77.6 - - - +
164A LYS* 1.3 64.0 + - - +
165A ASN* 5.3 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