Contacts of the helix formed by residues 135 - 147 (chain A) in PDB entry 6W6Y
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 ASP 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 GLY 3.9 0.8 + - - -
134A ALA* 1.3 72.2 - - - +
136A PRO* 1.3 70.5 - - - +
137A ILE* 3.1 23.3 + - - +
138A HIS* 3.0 22.4 + - + +
139A SER* 3.0 19.8 + - - -
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Residues in contact with PRO 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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126A LEU* 4.0 11.8 - - + +
129A ALA* 4.3 15.0 - - + -
130A GLY 5.7 1.8 - - - +
134A ALA 3.3 9.4 - - - +
135A ASP* 1.3 88.5 - - - +
137A ILE* 1.3 62.7 + - + +
139A SER* 3.2 4.1 + - - +
140A LEU* 3.0 19.4 + - - +
160A LEU* 3.5 40.2 - - + -
163A LYS* 6.0 2.5 - - + +
164A LEU* 3.5 14.3 - - + +
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Residues in contact with ILE 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 ASP* 3.1 11.7 + - - +
136A PRO* 1.3 79.8 - - + +
138A HIS* 1.3 63.1 + - - +
140A LEU* 3.4 4.2 + - + +
141A ARG* 3.1 51.6 + - + +
163A LYS* 4.2 27.1 - - + -
164A LEU* 3.8 18.2 - - + -
167A SER* 3.3 38.8 - - - +
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Residues in contact with HIS 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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106A ILE* 4.0 34.2 + - + +
109A LEU* 4.0 13.1 - - + +
134A ALA* 5.5 1.3 - - + -
135A ASP* 3.0 26.5 + - + +
137A ILE* 1.3 80.9 - - - +
139A SER* 1.3 62.6 + - - +
141A ARG* 3.1 18.4 + - + +
142A VAL* 2.9 44.3 + - + +
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Residues in contact with SER 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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109A LEU* 3.8 16.2 - - - -
113A TYR* 2.7 34.2 + - - -
126A LEU* 3.9 7.3 - - - +
127A LEU 2.6 31.6 + - - -
129A ALA* 4.9 2.2 - - - -
134A ALA* 5.3 2.0 - - - -
135A ASP 3.0 12.8 + - - -
136A PRO* 3.2 11.2 + - - -
138A HIS* 1.3 77.2 - - - +
140A LEU* 1.3 61.6 + - - +
142A VAL 3.3 1.0 + - - -
143A CYS 3.0 18.5 + - - -
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Residues in contact with LEU 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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12A LEU* 4.1 26.9 - - + -
16A VAL* 4.6 0.4 - - + -
18A ILE* 4.9 6.1 - - + -
126A LEU* 3.8 11.8 - - + +
136A PRO 3.0 16.3 + - - +
137A ILE* 3.7 5.4 - - + +
139A SER* 1.3 77.0 - - - +
141A ARG* 1.3 57.0 + - + +
143A CYS* 3.2 4.7 + - + +
144A VAL* 2.9 40.6 + - + +
153A LEU* 3.7 30.1 - - + -
164A LEU* 4.1 28.0 - - + +
168A PHE* 4.2 24.0 - - + -
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Residues in contact with ARG 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 ILE* 3.1 44.6 + - + +
138A HIS* 3.1 19.8 + - + +
140A LEU* 1.3 76.2 - - + +
142A VAL* 1.3 58.1 + - + +
144A VAL* 3.4 5.9 + - - +
145A ASP* 2.9 42.6 + - - +
167A SER* 3.8 11.1 + - - -
168A PHE* 5.5 11.4 - - + -
170A GLU* 5.6 2.6 + - - -
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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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109A LEU* 4.0 7.4 - - + -
110A LYS* 3.7 32.5 - - + +
113A TYR* 3.8 15.0 - - + -
138A HIS* 2.9 52.1 + - + +
139A SER 3.8 4.3 - - - +
141A ARG* 1.3 76.3 - - + +
143A CYS* 1.3 62.8 + - - +
145A ASP* 3.3 4.8 + - - -
146A THR* 2.7 40.9 + - - +
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Residues in contact with CYS 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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16A VAL* 4.6 3.9 - - - +
113A TYR* 3.5 41.2 - - + +
139A SER 3.0 11.6 + - - +
140A LEU* 3.4 13.7 - - + +
142A VAL* 1.3 75.8 - - - +
144A VAL* 1.3 59.2 + - - +
147A VAL* 2.9 40.2 + - - +
151A VAL* 4.0 28.7 - - - -
153A LEU* 4.3 20.4 - - + -
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Residues in contact with VAL 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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12A LEU* 5.2 0.9 - - + -
13A THR* 3.8 24.6 + - + +
15A ASN* 5.2 2.3 - - - +
16A VAL* 4.2 31.8 - - + +
140A LEU* 2.9 25.4 + - + +
141A ARG* 3.8 5.6 - - - +
142A VAL 3.3 0.2 - - - -
143A CYS* 1.3 79.6 - - - +
145A ASP* 1.3 68.2 + - - +
146A THR 3.6 0.2 + - - -
147A VAL 3.9 9.2 - - - +
168A PHE* 3.9 28.0 - - + -
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Residues in contact with ASP 145 (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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110A LYS* 5.1 3.7 + - - -
141A ARG* 2.9 27.6 + - - +
142A VAL* 3.9 5.0 - - - +
143A CYS 3.3 0.2 - - - -
144A VAL* 1.3 84.8 - - - +
146A THR* 1.3 62.6 + - - +
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Residues in contact with THR 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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110A LYS* 3.7 28.8 + - + +
113A TYR* 4.0 9.0 - - + -
114A GLU* 3.6 47.1 - - + +
117A ASN* 3.0 19.1 + - - -
142A VAL* 2.7 32.5 + - - +
145A ASP* 1.3 81.3 - - - +
147A VAL* 1.3 61.9 + - - +
148A ARG* 3.7 7.2 + - - +
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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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15A ASN* 2.8 22.6 + - - +
16A VAL* 4.8 0.4 - - + +
113A TYR* 3.6 38.4 - - + +
116A PHE* 3.9 23.6 - - + -
117A ASN* 3.4 6.3 - - - +
122A LEU* 5.3 0.2 - - + -
143A CYS* 2.9 20.3 + - - +
144A VAL 3.9 10.7 - - - +
145A ASP 5.2 0.2 - - - -
146A THR* 1.3 77.6 - - - +
148A ARG* 1.3 56.9 + - - +
149A THR* 3.6 32.1 - - - +
151A VAL* 4.0 16.8 - - + -
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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