Contacts of the helix formed by residues 140 - 156 (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 PRO 140 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128A GLU* 3.7 12.3 - - - +
132A HIS* 4.2 2.2 - - + +
139A ARG* 1.3 103.2 - - + +
141A LEU* 1.3 57.9 + - - +
142A VAL* 4.4 4.0 - - + +
143A GLU* 3.2 35.6 - - + +
144A THR* 2.7 37.2 + - - -
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Residues in contact with LEU 141 (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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122A GLN* 4.1 27.8 - - + +
126A THR* 3.6 23.6 - - + +
127A ASP* 4.2 1.8 - - - +
128A GLU* 3.3 36.2 + - + +
131A LEU* 3.5 32.1 - - + +
139A ARG 3.6 1.2 + - - -
140A PRO* 1.3 72.2 - - - +
142A VAL* 1.3 62.8 + - + +
144A THR* 3.2 2.4 + - - -
145A VAL* 2.9 39.5 + - + +
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Residues in contact with VAL 142 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140A PRO* 3.3 4.2 - - + +
141A LEU* 1.3 81.8 - - + +
143A GLU* 1.3 63.8 + - + +
145A VAL* 3.5 7.8 + - - +
146A ALA 3.3 15.2 + - - -
166A GLU* 5.4 16.2 - - + +
169A PHE* 3.6 30.5 - - + -
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Residues in contact with GLU 143 (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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139A ARG* 2.6 37.0 + - - +
140A PRO* 3.2 34.3 + - + +
141A LEU 3.3 0.4 - - - -
142A VAL* 1.3 79.4 - - + +
144A THR* 1.3 60.8 + - - +
146A ALA* 3.3 7.4 + - - +
147A HIS* 3.0 23.9 + - - +
169A PHE* 4.9 6.7 - - + -
173A ARG* 4.7 1.7 + - - -
136B TRP* 3.4 19.3 - - + -
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Residues in contact with THR 144 (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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122A GLN* 4.4 9.0 - - + +
131A LEU* 4.1 8.6 - - + +
137A ILE* 3.5 36.9 - - + +
139A ARG 3.6 3.5 + - - -
140A PRO 2.7 23.8 + - - -
141A LEU* 3.2 8.5 + - - -
143A GLU* 1.3 78.5 - - - +
145A VAL* 1.3 57.5 + - - +
147A HIS* 3.5 0.5 - - - +
148A TYR* 2.9 52.2 + - + +
136B TRP* 3.5 17.8 - - + -
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Residues in contact with VAL 145 (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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121A THR* 3.6 29.5 - - - +
122A GLN* 4.2 20.4 - - + +
141A LEU* 2.9 28.8 + - + +
142A VAL* 3.7 8.1 - - - +
143A GLU 3.3 0.2 - - - -
144A THR* 1.3 78.1 - - - +
146A ALA* 1.3 56.8 + - - +
148A TYR* 3.5 0.6 + - - -
149A ALA* 2.9 27.0 + - - +
162A CYS* 5.3 0.4 - - + -
166A GLU* 3.9 30.3 - - + +
169A PHE* 6.3 0.7 - - + -
170A ILE* 3.9 23.6 - - + -
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Residues in contact with ALA 146 (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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142A VAL 3.3 3.2 + - - -
143A GLU* 3.7 7.6 - - - +
144A THR 3.3 0.4 - - - -
145A VAL* 1.3 77.4 - - - +
147A HIS* 1.3 60.5 + - - +
149A ALA* 3.2 7.0 + - - +
150A ALA* 2.9 29.8 + - - +
169A PHE* 3.3 39.3 - - + -
170A ILE* 5.0 4.9 - - + -
173A ARG* 4.1 27.9 - - + +
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Residues in contact with HIS 147 (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* 5.4 3.8 - - - -
143A GLU 3.0 18.1 + - - +
144A THR 3.5 4.0 - - - +
145A VAL 3.3 0.2 - - - -
146A ALA* 1.3 77.8 - - - +
148A TYR* 1.3 65.2 + + - +
150A ALA* 3.1 8.7 + - - +
151A LEU* 2.9 44.8 + - + +
173A ARG* 4.0 13.0 + - - +
133B GLU 3.2 14.5 + - - -
134B GLU* 3.0 28.6 + - - -
136B TRP* 3.2 54.5 + + + -
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Residues in contact with TYR 148 (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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90A ALA* 3.7 24.1 - - + +
91A ALA* 4.1 20.8 - - + +
121A THR* 3.2 38.8 - - - +
122A GLN* 3.3 20.4 + - - -
137A ILE* 3.4 12.5 - - + +
144A THR* 2.9 30.7 + - + +
147A HIS* 1.3 86.5 - + - +
149A ALA* 1.3 61.5 + - - +
151A LEU* 3.2 11.9 + - + +
152A ALA* 3.1 18.4 + - - +
134B GLU 3.6 19.1 - - - -
135B LEU* 2.9 40.0 + - + +
136B TRP* 4.9 0.7 - - + -
137B ILE* 5.7 0.2 - - - +
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Residues in contact with ALA 149 (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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121A THR* 3.8 14.1 - - + +
145A VAL 2.9 18.8 + - - +
146A ALA* 3.5 7.6 - - - +
147A HIS 3.2 0.2 - - - -
148A TYR* 1.3 76.7 - - - +
150A ALA* 1.3 59.2 + - - +
152A ALA* 3.3 3.8 + - - +
153A LYS* 2.8 27.5 + - - +
160A VAL* 4.0 10.8 - - + -
170A ILE* 3.8 31.4 - - + -
174A CYS* 3.6 7.2 - - - -
178A PHE* 3.7 3.3 - - - -
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Residues in contact with ALA 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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146A ALA 2.9 13.7 + - - +
147A HIS* 3.1 11.6 + - - +
149A ALA* 1.3 75.6 - - - +
151A LEU* 1.3 54.5 + - + +
153A LYS* 3.1 1.9 + - - +
154A GLU* 2.7 51.0 + - + +
173A ARG* 3.5 24.9 - - + +
174A CYS* 3.7 13.9 - - - -
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Residues in contact with LEU 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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90A ALA* 4.7 12.1 - - + +
94A ARG* 3.1 47.2 - - + +
97A MET* 4.5 6.3 - - - -
147A HIS* 2.9 32.2 + - + +
148A TYR* 3.4 20.6 - - + +
150A ALA* 1.3 77.3 - - + +
152A ALA* 1.3 52.7 + - - +
154A GLU* 3.8 6.6 - - - +
155A SER* 2.7 37.3 + - - -
133B GLU 5.2 0.2 - - - +
134B GLU* 3.2 43.3 - - + +
135B LEU* 5.4 1.3 - - + -
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Residues in contact with ALA 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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97A MET* 3.8 13.9 - - + -
119A ALA* 3.6 31.0 - - + -
148A TYR 3.1 11.7 + - - +
149A ALA 3.5 8.3 - - - +
151A LEU* 1.3 74.1 - - - +
153A LYS* 1.3 66.4 + - - +
155A SER* 3.2 6.6 + - - -
156A GLY 3.4 0.2 + - - -
157A LEU* 3.1 31.2 + - + +
159A GLY 4.6 0.2 - - - +
160A VAL* 4.2 10.5 - - + -
178A PHE* 4.3 3.4 - - + -
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Residues in contact with LYS 153 (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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149A ALA 2.8 14.3 + - - +
150A ALA* 3.1 8.9 + - - +
152A ALA* 1.3 77.5 - - - +
154A GLU* 1.3 64.4 + - + +
156A GLY* 3.2 14.7 + - - -
157A LEU 4.3 3.3 + - - +
174A CYS* 3.2 41.3 + - + +
175A GLY* 5.6 0.2 - - - -
177A SER* 5.5 4.2 + - - -
178A PHE* 3.7 31.1 - - + +
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Residues in contact with GLU 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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94A ARG* 2.8 51.1 + - - +
98A GLU* 4.8 4.7 - - - +
150A ALA* 2.7 33.2 + - + +
151A LEU* 3.9 6.5 - - - +
153A LYS* 1.3 76.2 - - + +
155A SER* 1.3 59.5 + - - +
156A GLY 3.2 1.4 + - - -
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Residues in contact with SER 155 (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* 3.3 34.9 - - - +
97A MET* 3.6 26.3 - - - +
98A GLU* 3.6 28.6 - - - +
101A ILE* 4.3 3.5 - - - +
151A LEU 2.7 22.4 + - - -
152A ALA 3.7 6.1 - - - -
153A LYS 3.2 0.8 - - - -
154A GLU* 1.3 77.2 - - - +
156A GLY* 1.3 59.8 + - - +
157A LEU* 4.0 4.0 - - - +
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Residues in contact with GLY 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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101A ILE* 3.9 8.0 - - - +
114A ARG* 3.8 17.8 + - - -
153A LYS 3.2 7.8 + - - -
154A GLU 3.2 4.9 - - - -
155A SER* 1.3 81.9 - - - +
157A LEU* 1.3 66.7 + - - +
158A ASP* 4.5 1.2 - - - +
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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