Contacts of the helix formed by residues 135 - 147 (chain A) in PDB entry 1U1H
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 HIS 135 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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88A GLU* 2.7 43.1 + - - +
132A TYR* 3.5 38.3 - + - -
134A SER* 1.3 70.3 - - - +
136A LYS* 1.3 60.9 + - - +
137A ALA 3.2 3.4 - - - -
138A VAL* 3.3 15.3 - - + +
139A ASN* 2.8 40.7 + - - +
194A GLU* 3.3 31.5 + - - -
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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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60A ASN* 2.9 19.9 + - - +
62A PHE* 2.6 35.9 + - - -
63A ALA* 4.3 4.3 - - - +
64A HIS* 5.2 1.6 - - - +
70A ASP* 3.5 30.6 + - + +
74A MSE 6.4 0.4 - - + -
134A SER* 3.3 19.3 + - - +
135A HIS* 1.3 76.7 - - - +
137A ALA* 1.3 57.4 + - - +
139A ASN* 3.7 7.5 - - - +
140A GLU* 2.6 62.1 + - + +
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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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59A SER* 5.0 2.1 + - - -
60A ASN* 3.6 27.7 + - + +
74A MSE 3.8 28.5 - - + +
132A TYR* 6.0 0.2 - - - +
135A HIS 3.2 0.4 - - - -
136A LYS* 1.3 77.1 - - - +
138A VAL* 1.3 67.3 + - - +
140A GLU* 3.1 3.5 + - - +
141A TYR* 2.9 23.0 + - - +
153A PRO* 5.1 5.4 - - + +
155A LEU* 4.1 8.3 - - + -
191A VAL* 4.6 5.6 - - + -
195A LEU* 4.3 8.1 - - + -
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Residues in contact with VAL 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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132A TYR* 3.9 6.5 + - - +
135A HIS* 3.3 30.0 - - + +
137A ALA* 1.3 78.2 - - - +
139A ASN* 1.3 70.5 + - - +
141A TYR* 3.2 3.4 + - - +
142A LYS* 3.0 43.1 + - + +
194A GLU* 3.7 39.0 - - + +
195A LEU* 3.4 27.8 - - + +
198A ALA* 4.5 3.8 - - + -
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Residues in contact with ASN 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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88A GLU* 4.9 3.4 + - - -
135A HIS* 2.8 43.9 + - - +
136A LYS* 3.7 6.8 - - - +
138A VAL* 1.3 80.7 - - - +
140A GLU* 1.3 58.1 - - + +
142A LYS* 3.1 9.3 + - - +
143A GLU* 2.8 32.1 + - - +
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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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42A ARG* 3.5 31.7 + - - +
46A TRP* 3.5 18.4 - - + -
59A SER* 4.5 2.2 - - - -
60A ASN* 2.8 32.8 + - - +
62A PHE* 3.7 12.2 + - - +
136A LYS* 2.6 57.7 + - + +
137A ALA 3.7 3.1 - - - +
139A ASN* 1.3 77.1 - - + +
141A TYR* 1.3 63.9 + - - +
143A GLU* 4.2 6.7 - - - +
144A ALA* 3.0 26.3 + - - +
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Residues in contact with TYR 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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59A SER* 4.2 2.4 + - - +
137A ALA 2.9 13.1 + - - +
138A VAL* 3.4 11.7 - - - +
140A GLU* 1.3 77.3 - - - +
142A LYS* 1.3 61.0 + - + +
144A ALA* 3.5 2.4 + - - +
145A LYS* 2.9 45.4 + - + +
150A ASP* 2.6 23.6 + - - -
151A THR* 3.2 40.4 + - - -
153A PRO* 3.7 24.0 - - + -
195A LEU* 4.8 3.6 - - + -
198A ALA* 3.4 39.0 - - + -
199A GLY 2.9 7.6 + - - -
200A ALA* 2.8 36.7 + - + -
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Residues in contact with LYS 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 VAL* 3.0 28.7 + - + +
139A ASN* 3.7 7.2 - - - +
141A TYR* 1.3 76.1 - - + +
143A GLU* 1.3 65.9 + - - +
145A LYS* 3.1 9.2 - - + +
146A ALA* 2.9 24.3 + - - +
194A GLU 5.6 0.2 - - - -
198A ALA* 3.7 34.5 - - + +
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Residues in contact with GLU 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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39A ALA* 3.7 18.3 - - - +
42A ARG* 2.7 45.3 + - - -
46A TRP* 3.2 19.3 - - + -
139A ASN 2.8 20.7 + - - +
140A GLU* 3.7 5.4 - - - +
142A LYS* 1.3 73.8 - - - +
144A ALA* 1.3 61.4 + - - +
146A ALA* 3.3 7.2 + - - +
147A LEU* 3.1 37.2 + - + +
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Residues in contact with ALA 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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46A TRP* 3.5 28.9 - - + -
140A GLU 3.0 17.3 + - - +
141A TYR 3.8 3.1 - - - +
143A GLU* 1.3 74.4 - - - +
145A LYS* 1.3 66.8 + - - +
147A LEU* 3.2 3.2 + - - +
148A GLY 3.2 5.0 + - - -
149A VAL* 2.9 41.0 + - + +
151A THR* 3.7 19.3 - - + +
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Residues in contact with LYS 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 TYR* 2.9 46.1 + - + +
142A LYS* 3.1 15.7 - - + +
144A ALA* 1.3 76.2 - - - +
146A ALA* 1.3 54.8 + - - +
148A GLY* 2.7 27.7 + - - -
149A VAL 3.8 6.4 + - - +
150A ASP* 3.7 19.3 + - + +
198A ALA 3.9 14.6 - - - +
199A GLY* 4.0 14.3 + - - -
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Residues in contact with ALA 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 LYS 2.9 12.0 + - - +
143A GLU* 3.5 10.1 - - - +
145A LYS* 1.3 77.4 - - - +
147A LEU* 1.3 64.4 - - + +
148A GLY* 3.0 5.2 + - - -
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Residues in contact with LEU 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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43A SER* 3.5 44.2 - - - +
46A TRP* 3.6 22.7 - - + -
47A LYS* 4.1 24.5 - - - +
143A GLU* 3.1 24.0 + - + +
144A ALA* 3.2 7.6 + - - +
146A ALA* 1.3 79.0 - - + +
148A GLY* 1.3 59.0 + - - +
149A VAL* 3.9 7.0 + - + +
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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