Contacts of the helix formed by residues 126 - 143 (chain A) in PDB entry 4GR0
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 ASN 126 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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125A MET* 1.3 75.9 - - - +
127A ARG* 1.3 59.0 + - - +
128A GLU* 2.9 32.8 - - - +
129A ASP* 2.6 66.0 + - - +
130A VAL* 3.3 5.6 + - - +
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Residues in contact with ARG 127 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121A TYR* 3.5 64.3 + - + +
125A MET 3.6 2.5 + - - -
126A ASN* 1.3 73.5 - - - +
128A GLU* 1.3 71.6 + - - +
130A VAL* 3.2 6.8 + - - +
131A ASP* 3.1 28.5 + - - +
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Residues in contact with GLU 128 (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 ASN* 2.9 36.2 - - - +
127A ARG* 1.3 84.6 - - - +
129A ASP* 1.3 60.6 + - - +
131A ASP* 3.5 12.1 + - - +
132A TYR* 3.0 28.2 + - - +
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Residues in contact with ASP 129 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125A MET* 3.8 9.0 - - + +
126A ASN* 2.6 46.8 + - - +
128A GLU* 1.3 79.8 - - - +
130A VAL* 1.3 59.9 + - - +
132A TYR* 3.7 7.4 - - - +
133A ALA* 2.9 30.0 + - - +
205A THR* 3.6 30.9 - - + +
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Residues in contact with VAL 130 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118A ILE* 4.4 5.2 - - + -
121A TYR* 3.7 27.1 - - + -
122A THR* 4.0 20.2 - - + +
125A MET* 3.9 28.9 - - + -
126A ASN 3.3 5.5 + - - +
127A ARG* 3.2 8.2 + - - +
129A ASP* 1.3 75.4 - - - +
131A ASP* 1.3 65.4 + - - +
133A ALA* 3.3 1.0 + - - +
134A ILE* 3.0 31.5 + - + +
163A PHE* 4.1 16.4 - - + -
212A LEU* 3.9 17.5 - - + -
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Residues in contact with ASP 131 (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 TYR* 5.0 1.6 + - - -
118A ILE* 3.3 15.5 - - - +
121A TYR* 2.6 29.3 + - - -
127A ARG* 3.1 23.3 + - - +
128A GLU* 3.6 14.1 - - - +
130A VAL* 1.3 76.0 - - - +
132A TYR* 1.3 58.7 + - - +
134A ILE* 4.0 1.6 - - - +
135A ARG* 2.9 31.5 + - - +
151A LYS* 3.7 16.4 + - + +
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Residues in contact with TYR 132 (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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128A GLU 3.0 18.3 + - - +
129A ASP* 3.7 9.4 - - - +
130A VAL 3.2 0.2 - - - -
131A ASP* 1.3 77.2 - - - +
133A ALA* 1.3 66.0 + - - +
135A ARG* 3.1 38.3 + - - +
136A LYS* 3.0 62.9 + - + +
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Residues in contact with ALA 133 (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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125A MET* 4.7 3.1 - - + -
129A ASP 2.9 19.1 + - - +
130A VAL 3.3 3.3 + - - +
132A TYR* 1.3 78.6 - - - +
134A ILE* 1.3 59.5 + - - +
136A LYS* 3.5 2.6 + - - -
137A ALA* 3.0 28.8 + - - +
205A THR* 6.3 0.9 - - + -
212A LEU* 4.0 21.8 - - + -
213A PHE* 3.7 32.4 - - + +
216A ALA* 5.3 0.2 - - - -
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Residues in contact with ILE 134 (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 TYR* 3.7 28.7 - - + -
118A ILE* 4.2 17.7 - - + -
130A VAL* 3.0 24.7 + - + +
131A ASP 4.0 3.1 - - - +
133A ALA* 1.3 74.8 - - - +
135A ARG* 1.3 65.7 + - - +
137A ALA* 3.2 4.5 + - - +
138A PHE* 3.1 36.3 + - + -
161A VAL* 4.4 24.7 - - + -
163A PHE* 5.7 0.7 - - + -
197A PHE* 4.6 6.1 - - + -
212A LEU* 4.5 14.1 - - + -
216A ALA* 3.8 24.9 - - + -
220A ILE* 5.1 2.0 - - + -
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Residues in contact with ARG 135 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116A TYR* 3.8 18.3 + - - +
131A ASP 2.9 17.7 + - - +
132A TYR* 3.1 41.5 + - - +
134A ILE* 1.3 78.5 - - - +
136A LYS* 1.3 71.8 + - + +
138A PHE* 3.4 4.7 + - - +
139A GLN* 3.0 33.6 + - + +
151A LYS* 6.4 0.2 - - + -
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Residues in contact with LYS 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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132A TYR* 3.0 63.0 + - + +
133A ALA* 4.6 0.7 - - - -
135A ARG* 1.3 90.6 - - + +
137A ALA* 1.3 60.3 + - - +
139A GLN* 2.8 38.8 + - - +
140A VAL* 3.0 31.2 + - - +
213A PHE* 3.6 20.6 - - + -
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Residues in contact with ALA 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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133A ALA 3.0 18.5 + - - +
134A ILE 3.6 4.7 - - - +
136A LYS* 1.3 74.9 - - - +
138A PHE* 1.3 66.4 + - - +
140A VAL* 3.3 16.6 + - - +
141A TRP* 3.5 12.6 + - - -
213A PHE* 3.6 10.7 - - + +
216A ALA* 3.7 19.5 - - + -
217A VAL* 3.8 16.9 - - + +
220A ILE* 3.6 18.8 - - + -
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Residues in contact with PHE 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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116A TYR* 3.4 53.6 - + + -
134A ILE* 3.1 35.7 + - + -
135A ARG 3.7 6.5 - - - +
137A ALA* 1.3 77.1 - - - +
139A GLN* 1.3 58.4 + - - +
141A TRP* 3.1 4.2 + - - +
142A SER* 2.9 23.2 + - - -
149A PHE* 3.5 55.2 - + + -
159A ILE* 3.8 25.1 - - + -
161A VAL* 5.0 3.4 - - + -
220A ILE* 3.7 38.1 - - + -
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Residues in contact with GLN 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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135A ARG* 3.0 24.2 + - + +
136A LYS* 2.8 45.8 + - - +
138A PHE* 1.3 74.0 - - - +
140A VAL* 1.3 65.0 + - - +
142A SER* 3.0 11.8 + - - +
143A ASN* 2.9 50.3 + - - +
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Residues in contact with VAL 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 LYS 3.0 20.0 + - - +
137A ALA 3.4 9.4 - - - +
138A PHE 3.2 0.2 - - - -
139A GLN* 1.3 77.0 - - - +
141A TRP* 1.3 63.9 + - + +
143A ASN* 3.6 15.0 + - - +
144A VAL* 3.8 3.5 - - - +
213A PHE* 3.7 26.2 - - + -
217A VAL* 4.0 15.0 - - + -
248A PHE* 3.9 13.9 - - + -
250A LEU* 3.6 45.9 - - + +
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Residues in contact with TRP 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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137A ALA 3.5 20.6 - - - -
138A PHE 3.1 6.9 + - - +
140A VAL* 1.3 75.8 - - + +
142A SER* 1.3 64.0 + - - +
143A ASN 3.1 1.8 - - - -
144A VAL* 3.2 13.5 + - + +
145A THR* 2.9 20.3 + - + +
149A PHE* 4.4 4.5 - - + -
217A VAL* 2.8 39.1 + - + +
220A ILE* 3.6 20.9 - - + -
221A GLY* 3.6 16.9 - - - +
224A LEU* 3.9 20.6 - - + -
226A LEU* 3.5 26.9 - - + -
235A VAL* 3.9 20.6 - - + -
236A MET* 4.1 3.1 - - + -
250A LEU* 3.8 27.1 - - + -
254A ASP* 4.0 9.9 - - + -
258A ILE* 3.8 33.0 - - + -
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Residues in contact with SER 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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138A PHE 2.9 11.1 + - - -
139A GLN* 3.0 25.6 + - - +
141A TRP* 1.3 76.7 - - - +
143A ASN* 1.3 65.9 + - - +
145A THR* 3.1 21.2 - - - +
147A LEU 3.4 23.4 - - - +
148A LYS* 5.0 1.6 - - - -
149A PHE* 3.8 16.2 - - - -
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Residues in contact with ASN 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 GLN* 2.9 46.3 + - - +
140A VAL* 3.8 10.2 - - - +
141A TRP 3.1 0.6 - - - -
142A SER* 1.3 81.9 + - - +
144A VAL* 1.3 64.5 + - + +
145A THR 3.7 0.9 - - - -
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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