Contacts of the helix formed by residues 135 - 146 (chain A) in PDB entry 4ZGY
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 135 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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133A PHE* 3.8 5.1 - - - -
134A ASP* 1.3 92.3 - - - +
136A GLU* 1.3 68.7 + - - +
137A VAL* 3.2 9.4 + - - +
138A GLU* 3.6 14.7 + - - +
139A LEU* 3.1 25.6 + - - +
176A THR* 5.8 1.1 - - - -
180A LEU* 3.6 9.5 - - - +
153B LYS* 5.0 0.4 - - - -
154B ASP* 2.7 40.5 + - - -
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Residues in contact with GLU 136 (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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135A SER* 1.3 74.1 + - - +
137A VAL* 1.3 61.8 + - + +
139A LEU* 3.5 3.2 - - + +
140A MET* 2.9 49.6 + - + +
180A LEU* 3.6 18.1 - - + +
183A ARG* 3.2 39.3 + - + -
123B THR* 3.4 22.6 + - - +
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Residues in contact with VAL 137 (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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135A SER* 3.2 17.7 + - - +
136A GLU* 1.3 76.5 - - + +
138A GLU* 1.3 83.4 + - - +
140A MET* 3.3 17.6 + - + +
141A LYS* 2.9 40.1 + - + +
103B VAL* 5.2 3.8 - - + -
122B LEU* 4.2 15.9 - - + -
154B ASP* 3.9 13.0 - - + +
157B ALA* 4.2 12.1 - - + -
158B VAL* 3.9 26.0 - - + -
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Residues in contact with GLU 138 (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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113A PRO 3.7 10.2 - - - +
114A CYS* 3.6 4.4 - - - -
115A LYS* 2.9 40.2 + - + +
120A ILE* 4.6 2.0 - - + +
132A THR 5.2 1.1 - - - +
133A PHE* 4.0 18.8 - - + -
134A ASP* 4.1 11.0 - - - +
135A SER* 3.6 24.0 + - - +
136A GLU 3.4 0.2 - - - -
137A VAL* 1.3 82.9 - - + +
139A LEU* 1.3 57.5 + - - +
141A LYS* 2.9 34.5 + - - +
142A VAL* 2.9 34.8 + - + +
153B LYS* 4.7 3.1 - - - +
157B ALA* 3.9 9.4 - - - +
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Residues in contact with LEU 139 (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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133A PHE* 4.1 14.3 - - + -
135A SER 3.1 18.4 + - - +
136A GLU* 3.5 6.5 - - + +
138A GLU* 1.3 75.3 - - - +
140A MET* 1.3 59.8 + - + +
142A VAL* 3.2 6.1 + - - +
143A ALA* 2.9 26.2 + - - +
151A LEU* 3.6 26.7 - - + -
180A LEU* 3.9 22.9 - - + +
183A ARG* 3.7 37.9 - - + +
184A ALA* 4.0 15.9 - - + +
187A LEU* 4.4 7.6 - - + -
189A ILE* 4.5 11.9 - - + -
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Residues in contact with MET 140 (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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136A GLU* 2.9 41.8 + - + +
137A VAL* 3.9 19.5 - - + +
139A LEU* 1.3 77.2 - - + +
141A LYS* 1.3 59.0 + - + +
143A ALA* 3.4 8.2 + - - +
144A ARG* 2.9 28.1 + - - +
183A ARG* 4.3 17.3 - - - +
187A LEU* 4.5 14.4 - - + -
103B VAL* 5.4 10.3 - - + -
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Residues in contact with LYS 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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114A CYS* 4.9 0.8 - - - -
115A LYS 2.5 31.3 + - - +
116A GLN* 5.5 0.4 - - - +
117A VAL* 4.0 29.3 - - + +
120A ILE* 4.0 13.7 - - + +
137A VAL* 2.9 25.3 + - + +
138A GLU* 2.9 32.5 + - - +
140A MET* 1.3 75.8 - - + +
142A VAL* 1.3 59.9 + - - +
144A ARG* 3.1 10.8 + - - +
145A ALA* 2.9 31.4 + - - +
157B ALA* 4.4 17.4 + - - +
161B GLU* 4.0 16.5 + - + +
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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
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115A LYS* 5.5 1.3 - - + -
120A ILE* 4.0 14.1 - - + -
131A MET* 3.6 28.9 - - + -
132A THR 5.2 4.0 - - - +
133A PHE* 5.4 0.9 - - + -
138A GLU* 2.9 22.5 + - + +
139A LEU 3.5 5.4 - - - +
141A LYS* 1.3 73.1 - - - +
143A ALA* 1.3 61.3 + - - +
146A HIS* 2.8 50.9 + - + +
149A ALA* 4.4 2.7 - - + -
151A LEU* 3.7 39.5 - - + -
189A ILE* 4.4 8.3 - - + -
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Residues in contact with ALA 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 LEU 2.9 16.3 + - - +
140A MET* 3.7 5.6 - - - +
142A VAL* 1.3 77.2 - - - +
144A ARG* 1.3 61.2 + - - +
147A PRO* 4.2 14.4 - - - +
187A LEU* 4.0 25.4 - - + +
189A ILE* 3.7 27.6 - - + -
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Residues in contact with ARG 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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117A VAL* 4.5 28.3 - - + +
121A LYS* 4.8 3.3 + - - -
140A MET 2.9 18.7 + - - +
141A LYS* 3.2 9.6 - - - +
142A VAL 3.1 0.2 - - - -
143A ALA* 1.3 80.0 - - - +
145A ALA* 1.3 61.0 + - + +
147A PRO* 4.8 3.1 - - - +
165B GLU* 5.0 8.2 + - - -
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Residues in contact with ALA 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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117A VAL* 4.0 31.0 - - + +
120A ILE* 4.1 10.3 - - + -
121A LYS* 4.1 33.7 + - - +
124A ALA* 3.8 12.1 - - - +
141A LYS 2.9 12.0 + - - +
144A ARG* 1.3 76.9 - - + +
146A HIS* 1.3 61.5 + - - +
147A PRO* 3.6 8.5 - - - +
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Residues in contact with HIS 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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120A ILE* 3.6 19.3 - - + -
124A ALA* 3.4 31.2 - - + +
127A GLY 6.3 0.2 - - - -
128A VAL 2.9 23.3 + - - -
129A GLN* 3.6 17.8 + - - -
131A MET* 3.5 23.1 - - + -
142A VAL* 2.8 26.5 + - + +
145A ALA* 1.3 76.5 - - - +
147A PRO* 1.3 76.4 + - - +
148A LYS* 4.4 0.9 - - + -
149A ALA* 3.2 37.5 - - + +
189A ILE* 5.5 0.2 - - - +
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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