Contacts of the helix formed by residues 139 - 153 (chain A) in PDB entry 3GZN
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 139 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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44A ASN* 5.7 0.7 - - - +
137A GLN 3.9 5.6 - - - +
138A LEU* 1.4 91.3 - - + +
140A GLU* 1.3 67.0 + - - +
141A SER* 3.4 7.7 + - - +
142A THR* 3.4 22.2 + - - +
143A SER* 3.0 21.4 + - - -
161A ARG* 4.9 1.3 - - - +
440A ASP* 5.4 0.2 - - - +
443A HIS* 4.5 20.2 - - + +
449A TYR* 3.9 18.6 - - - +
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Residues in contact with GLU 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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139A PRO* 1.3 72.9 - - - +
141A SER* 1.3 57.6 + - - +
143A SER* 3.4 7.2 - - - -
144A LEU* 3.0 41.9 + - + +
409A TYR* 3.8 34.3 + - + +
437A ARG* 4.0 15.9 + - - +
440A ASP* 3.9 47.6 + - + +
441A ARG* 4.5 7.2 + - - +
443A HIS* 6.0 0.4 - - - -
444A LYS* 3.7 30.7 + - + +
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Residues in contact with SER 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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117A GLU* 4.8 8.3 + - - -
139A PRO* 4.6 6.8 - - - +
140A GLU* 1.3 78.6 + - - +
142A THR* 1.3 64.3 + - - +
144A LEU* 3.3 8.2 + - - +
145A ARG* 3.0 30.2 + - - +
444A LYS* 4.3 20.1 - - - +
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Residues in contact with THR 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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116A PRO* 4.0 22.9 - - + -
117A GLU* 2.7 31.6 + - + +
120A LEU* 4.7 4.4 - - + +
138A LEU* 3.7 25.4 - - + -
139A PRO* 3.4 28.1 + - + +
141A SER* 1.3 76.5 + - - +
143A SER* 1.3 60.6 + - - +
145A ARG* 3.3 3.0 + - - +
146A LEU* 2.9 35.4 + - + +
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Residues in contact with SER 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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138A LEU* 4.0 20.1 + - - +
139A PRO 3.0 18.0 + - - -
140A GLU* 3.4 9.6 - - - -
142A THR* 1.3 76.1 - - - +
144A LEU* 1.3 57.6 + - - +
146A LEU* 3.9 1.3 - - - +
147A ALA* 3.0 31.9 + - - +
157A LEU* 5.3 0.2 - - - +
159A ILE* 3.4 34.6 - - - +
405A LEU* 4.0 7.8 - - - +
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Residues in contact with LEU 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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140A GLU* 3.0 29.7 + - + +
141A SER* 3.8 6.1 - - - +
142A THR 3.2 0.2 - - - -
143A SER* 1.3 72.8 - - - +
145A ARG* 1.3 65.1 + - - +
147A ALA* 4.2 0.9 - - - +
148A ASP* 3.2 24.1 + - - +
405A LEU* 3.7 35.9 - - + +
406A ALA* 5.1 2.9 - - - +
409A TYR* 4.0 41.7 - - + -
444A LYS* 6.2 0.9 - - - +
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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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117A GLU* 3.3 37.1 + - - +
120A LEU* 3.0 45.3 + - + +
121A ASP* 2.6 37.9 + - - +
141A SER 3.0 16.5 + - - +
142A THR 3.7 3.8 - - - +
144A LEU* 1.3 73.3 - - - +
146A LEU* 1.3 66.2 + - - +
148A ASP* 3.4 4.8 + - - +
149A VAL* 3.1 34.4 + - + +
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Residues in contact with LEU 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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43A ILE* 3.6 27.6 - - + -
116A PRO* 6.2 2.9 - - + -
120A LEU* 3.9 16.6 - - + +
127A PHE* 4.1 30.7 - - + -
135A ALA* 3.8 18.6 - - + -
138A LEU* 4.0 8.1 - - + -
142A THR* 2.9 20.3 + - + +
143A SER* 3.9 2.0 - - - +
145A ARG* 1.3 74.0 - - - +
147A ALA* 1.3 61.9 + - - +
149A VAL* 3.3 2.1 + - - +
150A LEU* 2.9 54.1 + - + +
157A LEU* 3.9 17.7 - - + -
159A ILE* 5.9 0.4 - - + -
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Residues in contact with ALA 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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143A SER 3.0 18.9 + - - +
144A LEU 4.2 2.7 - - - +
146A LEU* 1.3 75.9 - - - +
148A ASP* 1.3 57.2 + - - +
150A LEU* 3.9 1.3 - - - +
151A TRP* 2.9 31.4 + - - +
157A LEU* 3.7 24.2 - - + +
172A ILE* 4.2 6.7 - - + +
405A LEU* 3.7 35.4 - - + +
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Residues in contact with ASP 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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144A LEU 3.2 17.2 + - - +
145A ARG* 3.7 5.4 - - - +
146A LEU 3.1 0.6 - - - -
147A ALA* 1.3 76.4 - - - +
149A VAL* 1.3 72.3 + - - +
151A TRP* 3.3 7.8 + - - +
152A ASN* 3.1 39.4 + - - +
406A ALA* 5.1 11.6 - - + +
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Residues in contact with VAL 149 (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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120A LEU* 3.8 26.0 - - + +
124A PRO* 4.3 29.8 - - + +
127A PHE* 5.2 0.4 - - + -
145A ARG* 3.1 21.8 + - - +
146A LEU 3.8 3.4 - - - +
148A ASP* 1.3 82.0 - - + +
150A LEU* 1.3 68.2 + - + +
152A ASN* 3.2 5.3 + - - +
153A SER* 2.8 41.4 + - - +
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Residues in contact with LEU 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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127A PHE* 3.5 37.2 - - + -
133A VAL* 3.8 31.0 - - + -
146A LEU* 2.9 31.8 + - + +
147A ALA 4.2 2.9 - - - +
149A VAL* 1.3 85.5 - - + +
151A TRP* 1.3 53.5 + - - +
153A SER* 4.0 3.8 - - - -
154A GLN* 2.7 27.5 + - - -
155A ILE* 2.8 40.5 + - + +
157A LEU* 3.8 27.1 - - + -
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Residues in contact with TRP 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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147A ALA 2.9 20.4 + - - +
148A ASP* 3.5 8.5 - - - +
149A VAL 3.2 0.2 - - - -
150A LEU* 1.3 76.9 - - - +
152A ASN* 1.3 71.2 + - - +
154A GLN* 3.1 22.5 + - - +
155A ILE 5.4 0.4 - - - -
172A ILE* 3.7 31.9 - - + -
174A LYS* 3.7 62.2 - - + +
402A CYS 3.3 26.9 - - - -
404A SER* 3.6 30.5 + - - -
407A GLU* 4.2 8.9 + - - -
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Residues in contact with ASN 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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148A ASP* 3.1 33.9 + - - +
149A VAL* 3.8 7.1 - - - +
151A TRP* 1.3 87.6 - - - +
153A SER* 1.3 58.8 + - - +
154A GLN* 3.2 5.1 + - - +
446C GLN* 4.8 11.4 + - - +
448C ARG* 3.5 19.3 + - - -
463C LYS* 3.5 18.6 + - - +
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Residues in contact with SER 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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124A PRO 5.6 0.9 + - - -
128A CYS* 4.2 10.5 - - - -
149A VAL* 2.8 30.8 + - - +
150A LEU* 3.8 6.7 - - - -
151A TRP 3.2 0.2 - - - -
152A ASN* 1.3 75.2 - - - +
154A GLN* 1.3 67.8 + - - +
155A ILE* 3.2 19.4 - - - +
446C GLN 5.6 0.5 + - - -
448C ARG* 3.8 17.8 + - - +
456C GLN* 2.5 35.0 + - - +
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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