Contacts of the helix formed by residues 140 - 154 (chain A) in PDB entry 2YZ2
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 140 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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139A LEU* 1.3 78.8 - - - +
141A GLY* 1.3 59.3 + - - +
142A GLY* 3.5 4.3 + - - -
143A GLU* 3.0 39.0 + - - +
144A LYS* 2.9 29.9 + - - +
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Residues in contact with GLY 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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88A GLU* 5.0 4.2 - - - +
139A LEU 3.9 0.6 + - - -
140A SER* 1.3 72.9 - - - +
142A GLY* 1.3 60.7 + - - +
144A LYS* 3.5 16.0 + - - +
145A ARG* 3.2 21.7 + - - +
169A LEU* 3.9 12.9 - - - +
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Residues in contact with GLY 142 (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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140A SER* 3.3 5.3 + - - -
141A GLY* 1.3 75.8 - - - +
143A GLU* 1.3 62.1 + - - +
145A ARG* 3.4 3.7 + - - +
146A ARG* 3.0 37.5 + - - +
169A LEU* 4.1 15.0 - - - +
170A ASP* 5.7 1.8 + - - -
173A GLY* 4.6 17.5 - - - -
177A LEU* 4.8 0.6 - - - +
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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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126A LEU* 3.9 14.4 - - + +
131A PHE* 3.6 22.1 - - + -
134A ARG* 4.7 3.9 + - - -
139A LEU* 3.5 23.6 - - + +
140A SER* 3.0 36.9 + - - +
142A GLY* 1.3 73.8 - - - +
144A LYS* 1.3 60.6 + - - +
146A ARG* 3.2 27.6 + - - +
147A VAL* 2.9 33.6 + - - +
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Residues in contact with LYS 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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88A GLU* 3.7 26.2 - - + -
91A PHE* 3.3 24.2 - - + -
136A PRO 3.6 26.5 - - - +
137A PHE* 4.2 12.9 + - - +
139A LEU* 3.7 19.8 + - + +
140A SER 2.9 22.0 + - - +
141A GLY* 3.9 14.1 - - - +
142A GLY 3.3 0.2 - - - -
143A GLU* 1.3 73.8 - - - +
145A ARG* 1.3 65.4 + - - +
147A VAL* 3.3 4.0 + - - -
148A ALA* 3.1 19.1 + - - +
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Residues in contact with ARG 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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86A TYR* 3.7 17.7 - - - +
87A PRO* 3.6 19.0 - - - +
88A GLU* 2.9 45.3 + - - +
141A GLY 3.2 10.5 + - - +
142A GLY 3.5 9.0 - - - +
143A GLU 3.3 0.2 - - - -
144A LYS* 1.3 79.6 - - - +
146A ARG* 1.4 52.0 + - - +
148A ALA* 3.3 5.1 + - - +
149A ILE* 2.8 42.6 + - + +
164A GLU 4.8 0.4 - - - -
165A PRO* 3.1 28.9 + - - +
167A VAL* 2.2 48.4 + - - +
168A GLY* 5.5 0.2 - - - -
169A LEU* 3.4 21.6 - - + +
177A LEU* 3.8 22.9 - - + -
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Residues in contact with ARG 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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124A VAL* 2.9 47.2 + - + +
125A GLY* 3.4 20.8 + - - -
126A LEU* 3.6 15.8 - - + +
131A PHE* 5.7 0.2 - - - -
142A GLY* 3.0 18.6 + - - +
143A GLU* 3.5 34.5 - - - +
144A LYS 3.1 0.4 - - - -
145A ARG* 1.4 71.8 - - - +
147A VAL* 1.4 58.4 + - - +
149A ILE* 3.1 6.3 + - - +
150A ALA 2.8 25.1 + - - -
173A GLY* 6.0 0.2 - - - -
176A ASP* 3.3 41.2 + - - +
177A LEU* 4.0 10.3 - - + -
180A ILE* 3.6 22.9 - - + -
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Residues in contact with VAL 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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91A PHE* 3.8 19.1 - - + -
96A VAL* 3.7 33.0 - - + -
99A GLU* 4.4 10.8 - - + -
100A VAL* 3.9 9.6 - - + +
126A LEU* 3.5 19.5 - - + +
131A PHE* 5.8 0.4 - - + -
136A PRO* 5.4 2.5 - - + -
139A LEU* 3.9 21.1 - - + -
143A GLU 2.9 19.5 + - - +
144A LYS 3.3 6.3 + - - +
146A ARG* 1.4 74.4 - - - +
148A ALA* 1.3 57.1 + - - +
150A ALA* 3.2 7.8 + - - +
151A SER* 3.0 26.9 + - - -
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Residues in contact with ALA 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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87A PRO* 3.6 18.2 - - + +
88A GLU 3.5 28.0 - - - +
91A PHE* 3.7 13.6 - - + -
144A LYS 3.1 9.0 + - - +
145A ARG 3.3 9.9 - - - +
147A VAL* 1.3 75.9 - - - +
149A ILE* 1.3 67.4 + - - +
151A SER* 2.9 20.5 + - - -
152A VAL* 3.3 13.9 + - - +
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Residues in contact with ILE 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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83A ALA* 3.9 14.4 - - + -
87A PRO* 4.6 7.0 - - + -
124A VAL* 3.9 16.8 - - + -
145A ARG* 2.8 31.6 + - + +
146A ARG* 3.1 8.3 + - - +
148A ALA* 1.3 71.8 - - - +
150A ALA* 1.3 65.5 + - - +
152A VAL* 2.7 18.7 + - + +
153A ILE* 3.0 24.9 + - + +
160A LEU* 4.9 4.3 - - + -
162A LEU* 3.5 32.5 - - + -
165A PRO* 5.8 1.6 - - + -
177A LEU* 4.5 19.7 - - + -
180A ILE* 4.2 19.3 - - + -
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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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100A VAL* 3.9 17.0 - - + -
120A ALA* 3.5 16.9 - - - +
121A MET* 4.1 4.5 - - + +
124A VAL* 3.7 24.3 - - + +
126A LEU* 5.5 0.2 - - + -
146A ARG 2.8 17.1 + - - +
147A VAL* 3.4 12.3 - - - +
149A ILE* 1.3 71.9 - - - +
151A SER* 1.3 58.2 + - - +
153A ILE* 3.4 7.1 + - - +
154A VAL* 3.0 31.7 + - - +
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Residues in contact with SER 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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91A PHE* 5.6 0.2 - - - -
99A GLU* 4.2 16.8 + - - +
100A VAL* 3.8 27.8 - - - -
103A ALA* 3.3 24.5 - - - +
147A VAL 3.0 11.9 + - - -
148A ALA* 2.9 18.2 + - - -
149A ILE 3.0 0.2 - - - -
150A ALA* 1.3 78.7 - - - +
152A VAL* 1.3 62.3 + - - +
154A VAL* 3.6 5.3 - - - +
155A HIS* 5.2 0.9 - - - -
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Residues in contact with VAL 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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81A GLY* 3.5 38.1 - - - +
82A ILE 3.6 20.9 - - - +
83A ALA* 4.1 12.1 - - + +
84A PHE* 4.9 8.7 - - + -
87A PRO* 5.6 1.1 - - + -
148A ALA 3.5 12.6 - - - +
149A ILE* 2.7 17.9 + - - +
151A SER* 1.3 77.5 + - - +
153A ILE* 1.3 56.4 + - - +
155A HIS* 3.5 23.9 + - - -
157A PRO* 4.1 0.2 - - - +
160A LEU* 4.3 11.4 - - + -
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Residues in contact with ILE 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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120A ALA* 4.5 6.0 - - + +
123A PHE* 3.9 29.2 - - + -
124A VAL* 3.9 27.1 - - + -
149A ILE* 3.0 15.0 + - + +
150A ALA* 3.5 10.5 - - - +
152A VAL* 1.3 75.7 - - + +
154A VAL* 1.3 70.7 + - - +
155A HIS 3.2 2.7 - - - -
156A GLU* 2.8 18.3 + - - +
157A PRO* 3.8 8.3 - - + -
160A LEU* 3.9 23.6 - - + -
180A ILE* 5.6 0.4 - - + -
184A TRP* 3.5 32.4 - - + -
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Residues in contact with VAL 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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100A VAL* 3.8 14.6 - - + +
103A ALA* 3.4 43.3 - - + +
104A VAL* 3.7 23.1 - - + -
116A LEU* 3.6 45.0 - - + +
117A VAL* 4.0 0.9 - - - +
120A ALA* 3.7 13.4 - - + +
150A ALA 3.0 17.0 + - - +
151A SER 3.6 5.2 - - - +
152A VAL 3.4 1.0 - - - -
153A ILE* 1.3 78.1 - - - +
155A HIS* 1.3 64.9 + - + +
156A GLU* 3.3 3.8 + - - +
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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