Contacts of the helix formed by residues 128 - 147 (chain A) in PDB entry 6DWM
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 GLY 128 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104A LYS* 5.2 4.0 - - - -
126A ASP* 3.0 10.6 + - - -
127A SER* 1.3 83.0 - - - +
129A PRO* 1.3 75.0 - - - +
130A VAL 3.3 2.2 + - - -
131A TRP* 3.4 2.9 + - - -
132A ALA* 3.3 17.2 + - - +
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Residues in contact with PRO 129 (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 GLY* 1.3 81.2 - - - +
130A VAL* 1.3 72.0 + - + +
132A ALA* 3.3 8.3 + - + +
133A ALA* 3.0 24.8 + - - +
136A ARG* 5.6 0.2 + - - -
301A GLN* 5.8 8.1 - - - +
393B ASP* 5.6 9.4 - - + +
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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
----------------------------------------------------------
126A ASP* 3.2 21.1 + - - +
128A GLY 3.3 0.8 - - - -
129A PRO* 1.3 83.6 - - + +
131A TRP* 1.3 63.1 + - - +
133A ALA* 3.4 4.3 + - - +
134A ARG* 3.2 35.0 + - - +
301A GLN* 4.7 26.0 - - - +
302A LEU* 3.4 27.3 - - + +
306A LYS* 4.6 17.5 - - + +
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Residues in contact with TRP 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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104A LYS* 4.8 13.5 - - + -
121A MET* 3.4 32.0 + - + +
126A ASP* 3.2 31.9 + - - +
127A SER* 3.7 20.6 - - - -
128A GLY 3.4 6.8 + - - +
129A PRO 3.3 0.4 - - - -
130A VAL* 1.3 79.2 - - - +
132A ALA* 1.3 83.7 + - + +
134A ARG* 3.1 11.0 + - - +
135A ARG* 2.8 56.3 + - - +
454A LYS* 3.5 28.5 - - + -
455A ARG* 3.3 49.0 - - - +
601A HEM 3.6 6.4 + - - -
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Residues in contact with ALA 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 GLY 3.3 10.3 + - - +
129A PRO* 3.8 10.5 - - + +
131A TRP* 1.3 99.8 - - + +
133A ALA* 1.3 56.9 + - - +
135A ARG* 3.5 4.8 + - - +
136A ARG* 2.8 42.5 + - + +
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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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129A PRO 3.0 17.0 + - - +
130A VAL* 3.6 7.0 - - - +
131A TRP 3.2 0.2 - - - -
132A ALA* 1.3 75.3 - - - +
134A ARG* 1.3 64.7 + - - +
136A ARG* 3.1 30.2 + - - +
137A LEU* 3.0 27.0 + - + +
301A GLN* 6.4 0.4 - - - +
302A LEU* 4.5 17.3 - - + -
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Residues in contact with ARG 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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119A GLN* 2.7 31.7 + - - +
120A SER 4.2 3.2 + - - -
121A MET* 3.3 38.1 - - + +
124A SER* 4.5 6.9 + - - -
126A ASP* 4.6 8.7 + - - +
130A VAL* 3.2 27.8 - - - +
131A TRP* 3.1 9.9 + - - +
133A ALA* 1.3 75.4 - - - +
135A ARG* 1.3 64.4 + - - +
137A LEU* 3.1 8.2 + - - +
138A ALA* 3.0 21.3 + - - +
302A LEU* 4.1 15.5 - - + -
306A LYS* 3.1 40.5 + - - +
309A ASN* 3.0 21.6 + - - +
310A ILE* 3.5 23.7 - - + +
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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
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121A MET* 3.7 11.8 - - + -
131A TRP* 2.8 46.4 + - + +
132A ALA* 3.8 7.2 - - - +
134A ARG* 1.3 75.2 - - - +
136A ARG* 1.3 60.4 + - + +
138A ALA* 3.4 2.9 + - - +
139A GLN* 3.1 44.5 + - - +
453A GLY 4.6 0.4 + - - -
454A LYS 3.4 20.2 + - - -
455A ARG 3.9 0.6 - - - -
456A LYS* 2.8 43.4 + - - +
457A CYS 4.7 0.2 + - - -
458A ILE* 3.3 32.9 - - + +
601A HEM 3.0 27.6 + - - +
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Residues in contact with ARG 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 ALA* 2.8 30.0 + - + +
133A ALA* 3.1 28.2 + - - +
135A ARG* 1.3 76.8 - - + +
137A LEU* 1.3 63.2 + - - +
139A GLN* 4.1 13.3 - - - +
140A ASN* 3.2 35.9 + - - +
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Residues in contact with LEU 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 17.2 + - + +
134A ARG* 3.1 6.9 + - - +
136A ARG* 1.3 76.6 - - + +
138A ALA* 1.3 59.5 + - - +
140A ASN* 3.6 4.7 + - + +
141A GLY* 3.0 26.0 + - - -
281A ILE* 5.9 0.7 - - - +
284A SER 5.9 0.7 - - - +
285A LEU* 4.5 14.7 - - + +
288A HIS* 3.8 50.0 - - + +
302A LEU* 4.3 14.4 - - + -
307A ILE* 4.3 16.4 - - + -
310A ILE* 4.4 15.9 - - + -
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Residues in contact with ALA 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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121A MET* 4.4 4.9 - - + -
134A ARG 3.0 11.4 + - - +
135A ARG 3.8 3.1 - - - +
137A LEU* 1.3 74.9 - - - +
139A GLN* 1.3 60.6 + - - +
141A GLY* 3.7 0.8 - - - -
142A LEU* 2.8 36.1 + - - +
281A ILE* 6.2 0.7 - - - -
285A LEU* 6.3 0.2 - - - -
310A ILE* 3.7 27.1 - - + +
314A LEU* 4.1 13.8 - - + +
458A ILE* 3.7 23.3 - - + -
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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* 3.1 37.5 + - - +
136A ARG* 4.1 15.6 - - - +
138A ALA* 1.3 77.2 - - - +
140A ASN* 1.3 60.7 + - - +
142A LEU* 3.6 8.1 - - - +
143A LYS* 2.8 32.6 + - - +
458A ILE* 3.8 33.9 - - + +
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Residues in contact with ASN 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 ARG* 3.2 24.0 + - - +
137A LEU* 4.2 5.4 - - + +
138A ALA 3.3 0.4 - - - -
139A GLN* 1.3 77.4 - - - +
141A GLY* 1.3 60.8 + - - +
143A LYS* 3.7 24.6 + - - +
144A SER* 2.7 40.3 + - - +
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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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137A LEU 3.0 18.4 + - - -
138A ALA 3.7 0.9 - - - -
140A ASN* 1.3 77.5 - - - +
142A LEU* 1.3 60.7 + - - +
144A SER* 4.6 3.4 - - - -
145A PHE* 3.2 27.5 + - - -
281A ILE* 3.4 22.9 - - - +
284A SER* 4.5 13.9 - - - -
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Residues in contact with LEU 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 ALA 2.8 19.6 + - - +
139A GLN* 3.6 5.2 - - - +
141A GLY* 1.3 73.7 - - - +
143A LYS* 1.3 56.3 + - - +
145A PHE 3.2 1.2 + - - -
146A SER* 2.4 40.7 + - - -
198A ILE* 5.0 3.4 - - + -
201A ILE* 4.8 7.2 - - + -
281A ILE* 4.0 18.5 - - + +
314A LEU* 4.1 18.8 - - + -
458A ILE* 3.5 44.6 - - + +
462A ILE* 3.6 25.8 - - + -
601A HEM 3.9 19.3 - - + -
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Residues in contact with LYS 143 (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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139A GLN* 2.8 19.8 + - - +
140A ASN* 3.7 24.5 + - - +
142A LEU* 1.3 73.4 - - - +
144A SER* 1.3 68.9 + - - +
146A SER* 3.9 4.5 - - - -
147A ILE* 3.3 27.3 + - + +
148A ALA* 3.3 21.1 + - - +
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Residues in contact with SER 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 ASN* 2.7 30.4 + - - +
141A GLY* 4.6 0.2 - - - -
143A LYS* 1.3 81.5 + - - +
145A PHE* 1.3 80.8 + - - +
146A SER 3.6 0.2 - - - -
148A ALA* 3.2 24.3 - - - +
158A TYR* 3.8 8.1 - - - -
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Residues in contact with PHE 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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141A GLY* 3.2 19.3 + - - +
142A LEU 3.2 3.9 + - - -
144A SER* 1.3 94.5 - - - +
146A SER* 1.3 58.7 + - - +
158A TYR* 3.5 37.1 - + + +
162A HIS* 5.1 0.2 + - - -
201A ILE* 3.5 38.1 - - + +
278A ILE* 3.5 37.5 - - + -
279A ARG 3.5 11.0 - - - -
280A ASP* 3.4 36.3 - - - -
281A ILE* 4.1 6.3 - - + -
284A SER* 4.3 12.3 - - - -
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Residues in contact with SER 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 LEU* 2.4 29.1 + - - -
143A LYS* 3.9 0.3 - - - -
144A SER 3.6 0.6 - - - -
145A PHE* 1.3 79.5 - - - +
147A ILE* 1.3 78.3 + - - +
148A ALA 3.5 0.9 - - - -
157A CYS* 3.7 2.6 - - - -
158A TYR* 3.6 7.6 + - - -
159A LEU* 3.0 37.7 + - - +
201A ILE* 4.2 12.8 - - - -
462A ILE* 3.4 30.1 - - - +
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Residues in contact with ILE 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 LYS* 3.3 27.8 + - + +
146A SER* 1.3 89.2 + - - +
148A ALA* 1.3 68.8 + - - +
149A SER* 3.7 0.9 + - - -
157A CYS* 3.3 15.4 - - - +
159A LEU* 6.3 0.2 - - + -
461A THR* 4.1 21.8 - - + +
462A ILE* 5.2 4.0 - - + -
465A TRP* 4.0 37.2 - - + -
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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