Contacts of the helix formed by residues 131 - 141 (chain A) in PDB entry 4U86
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 GLN 131 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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68A ARG* 2.9 23.6 + - - -
130A MET* 1.3 73.8 - - - +
132A LYS* 1.3 68.4 + - - +
133A PRO* 3.5 8.7 - - + -
134A PHE* 3.0 8.3 + - + +
135A GLU* 2.9 19.2 + - - +
152A THR* 3.2 29.3 + - + +
153A ASP* 3.7 17.2 - - - +
154A SER* 2.9 21.9 + - - -
157A HIS* 4.5 4.2 + - - -
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Residues in contact with LYS 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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127A ARG* 3.6 5.1 - - - +
130A MET 3.5 4.3 + - - -
131A GLN* 1.3 72.1 - - - +
133A PRO* 1.4 62.9 - - + +
135A GLU* 3.3 25.5 + - - +
136A ASP* 2.8 68.7 + - - +
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Residues in contact with PRO 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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28A ILE 4.9 2.1 - - - +
131A GLN* 3.5 8.7 - - + -
132A LYS* 1.4 94.3 - - + +
134A PHE* 1.3 55.6 + - - +
136A ASP* 4.1 5.4 - - + +
137A ALA* 3.1 30.3 + - - +
150A VAL* 3.7 10.4 - - + +
151A PHE 3.3 26.9 - - - +
152A THR* 4.2 9.0 - - + -
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Residues in contact with PHE 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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57A CYS* 4.8 2.7 - - + -
59A HIS* 3.6 14.6 - + + -
122A LEU* 3.6 28.9 - - + -
125A PHE* 3.9 12.6 - + - -
130A MET* 4.1 22.2 - - + -
131A GLN* 3.0 14.2 + - + +
133A PRO* 1.3 79.2 - - - +
135A GLU* 1.4 64.7 + - - +
137A ALA* 3.4 2.3 + - - +
138A SER* 2.9 43.9 + - - -
150A VAL* 4.4 1.6 - - - -
152A THR* 4.1 11.8 - - + +
157A HIS* 3.5 37.5 - + + -
159A ILE* 3.6 37.5 - - + +
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Residues in contact with GLU 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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125A PHE* 4.8 3.1 - - + -
126A SER 5.2 1.1 - - - +
127A ARG* 2.9 37.1 + - + +
128A GLY* 2.9 31.2 + - - -
129A GLN 4.1 1.4 + - - -
130A MET* 3.9 19.9 + - + +
131A GLN 2.9 11.8 + - - +
132A LYS* 3.3 27.1 + - - +
134A PHE* 1.4 78.7 - - - +
136A ASP* 1.4 62.8 + - - +
138A SER* 3.1 5.5 + - - -
139A PHE* 2.9 43.1 + - + -
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Residues in contact with ASP 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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28A ILE* 3.5 16.7 - - + +
127A ARG* 2.9 20.1 + - - +
132A LYS* 2.8 59.8 + - - +
133A PRO* 4.1 5.8 - - + +
135A GLU* 1.4 71.4 - - - +
137A ALA* 1.3 63.6 + - - +
139A PHE* 3.5 1.6 + - - +
140A ALA* 3.1 24.9 + - - +
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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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28A ILE* 3.7 23.5 - - - +
29A THR* 3.6 10.3 - - + +
133A PRO 3.1 19.2 + - - +
134A PHE 3.8 2.9 - - - +
136A ASP* 1.3 78.6 - - - +
138A SER* 1.3 63.2 + - - +
140A ALA 3.2 0.5 + - - -
141A LEU* 3.1 29.4 + - - +
147A SER* 5.1 2.0 - - - -
150A VAL* 3.9 13.0 - - + -
159A ILE* 3.9 17.7 - - + -
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Residues in contact with SER 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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55A VAL* 4.1 5.6 - - - +
57A CYS* 3.6 23.3 - - - -
125A PHE* 3.8 15.0 - - - -
134A PHE* 2.9 42.4 + - - -
135A GLU 3.1 4.2 + - - -
137A ALA* 1.3 78.3 - - - +
139A PHE* 1.3 62.3 + - - +
141A LEU* 3.6 13.0 + - - +
159A ILE* 3.9 4.8 - - - +
161A ARG* 3.7 21.7 - - - +
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Residues in contact with PHE 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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51A GLU* 3.8 27.3 - - + +
52A PRO* 3.5 26.6 - - + +
53A ALA 4.0 6.7 - - - -
55A VAL* 3.9 35.2 - - + +
125A PHE* 3.8 30.7 - + - -
126A SER 4.1 0.7 - - - -
127A ARG* 3.4 60.1 - - + +
135A GLU* 2.9 28.3 + - + +
136A ASP 4.3 0.2 - - - +
138A SER* 1.3 80.6 - - - +
140A ALA* 1.3 57.6 + - - +
141A LEU 3.4 5.1 - - - +
161A ARG* 4.7 4.4 + - - -
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Residues in contact with ALA 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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11A TRP* 5.8 1.2 + - - -
26A ASN* 5.0 9.0 + - - +
28A ILE* 3.8 22.7 - - + -
29A THR* 3.7 21.9 - - + +
127A ARG* 5.5 0.2 - - - +
136A ASP 3.1 18.6 + - - +
137A ALA 3.2 0.4 + - - -
139A PHE* 1.3 72.6 - - - +
141A LEU* 1.3 65.0 + - - +
142A ARG* 3.7 4.5 + - - +
145A GLU* 4.4 2.3 - - - +
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Residues in contact with LEU 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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29A THR* 3.8 16.8 - - + -
137A ALA 3.1 19.5 + - - +
138A SER* 3.8 8.7 - - - +
139A PHE 3.4 4.2 - - - +
140A ALA* 1.3 79.2 - - - +
142A ARG* 1.3 65.9 + - - +
145A GLU* 3.5 37.7 - - + +
146A MET 3.7 19.1 - - - +
147A SER* 3.7 7.0 - - - +
159A ILE* 3.8 36.8 - - + +
161A ARG* 2.9 34.8 + - + +
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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