Contacts of the helix formed by residues 137 - 153 (chain D) in PDB entry 1UHG
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 ALA 137 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133D ASN* 3.3 21.0 + - + +
136D THR* 1.3 86.7 + - - +
138D ALA* 1.3 53.2 + - - +
139D ASP 3.3 2.5 - - - -
140D GLN* 3.0 32.4 + - + +
141D ALA 2.8 30.1 + - - -
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Residues in contact with ALA 138 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134D PHE* 3.4 22.9 + - - +
135D GLN 5.3 0.2 + - - -
136D THR 3.8 0.8 - - - -
137D ALA* 1.3 75.9 - - - +
139D ASP* 1.3 58.5 + - - +
141D ALA* 3.3 7.7 + - - +
142D ARG 3.0 23.2 + - - -
166D VAL* 3.4 15.9 - - + +
167D ASP* 3.5 35.0 - - - +
168D SER* 3.9 2.0 - - - +
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Residues in contact with ASP 139 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137D ALA 3.3 0.6 - - - -
138D ALA* 1.3 78.5 - - - +
140D GLN* 1.3 60.6 + - - +
142D ARG* 3.5 27.4 + - - +
143D GLU* 3.3 20.3 + - - +
164D DSN 5.7 2.4 + - - -
166D VAL* 5.2 1.3 - - - +
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Residues in contact with GLN 140 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189C LYS* 2.8 32.9 + - - +
341C VAL* 3.9 23.0 + - + +
132D ILE* 4.7 3.4 - - - +
133D ASN* 4.2 7.6 + - - +
137D ALA* 3.0 32.3 + - + +
139D ASP* 1.3 74.8 - - - +
141D ALA* 1.3 84.6 + - - +
143D GLU* 3.2 5.9 + - - +
144D LEU* 3.0 43.8 + - + +
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Residues in contact with ALA 141 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132D ILE* 3.2 29.4 - - + +
133D ASN 3.7 13.5 - - - +
134D PHE* 3.7 20.0 - - + -
137D ALA 2.8 13.1 + - - +
138D ALA 3.5 8.7 - - - +
140D GLN* 1.3 81.4 - - - +
142D ARG* 1.3 62.0 + - - +
144D LEU* 3.2 1.0 + - - -
145D ILE* 2.9 30.7 + - - +
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Residues in contact with ARG 142 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138D ALA 3.0 7.1 + - - +
139D ASP* 3.6 28.4 + - - +
140D GLN 3.2 0.2 - - - -
141D ALA* 1.3 76.2 - - - +
143D GLU* 1.3 59.3 + - - +
145D ILE* 3.8 5.8 - - - +
146D ASN* 2.8 50.9 + - - +
159D ASN* 5.3 5.3 + - - +
161D LEU* 3.2 47.7 + - + -
162D GLN 3.8 7.5 + - - -
163D PRO* 3.4 41.2 - - - +
164D DSN 4.6 2.4 + - - -
165D SER* 4.3 0.7 - - - +
166D VAL* 3.3 30.6 - - + +
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Residues in contact with GLU 143 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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188C PHE 3.9 5.0 - - - +
189C LYS* 3.6 25.2 + - - +
190C ASP* 2.9 59.0 + - - +
191C GLU* 4.7 2.6 + - - +
336C GLU* 5.4 0.2 - - - +
139D ASP 3.3 9.7 + - - +
140D GLN* 3.2 10.1 + - - +
142D ARG* 1.3 79.7 - - - +
144D LEU* 1.3 61.1 + - + +
146D ASN* 4.0 5.0 - - - +
147D SER* 2.9 38.3 + - - +
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Residues in contact with LEU 144 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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187C ALA* 4.4 5.4 - - + -
189C LYS* 5.7 0.4 - - - +
338C GLY 3.6 24.3 - - - +
339C ARG 3.7 17.0 - - - +
340C GLU* 4.0 14.4 - - - -
341C VAL* 4.4 14.6 - - + +
106D TYR* 5.0 3.1 - - + -
132D ILE* 4.1 18.6 - - + -
140D GLN* 3.0 48.1 + - + +
141D ALA 3.2 4.2 + - - +
143D GLU* 1.3 76.3 - - + +
145D ILE* 1.3 58.6 + - - +
147D SER* 2.8 18.7 + - - +
148D TRP* 2.9 19.1 + - - +
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Residues in contact with ILE 145 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106D TYR* 3.7 52.3 - - + -
132D ILE* 4.1 3.8 - - + -
134D PHE* 3.9 26.0 - - + -
141D ALA 2.9 20.6 + - - +
142D ARG* 3.8 3.4 - - - +
144D LEU* 1.3 76.1 - - - +
146D ASN* 1.3 63.8 + - - +
148D TRP* 3.1 3.3 + - - +
149D VAL* 3.1 23.6 + - + +
161D LEU* 3.4 33.4 - - + -
166D VAL* 5.3 0.4 - - + -
173D VAL* 4.6 3.8 - - + -
175D VAL* 3.7 23.8 - - + -
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Residues in contact with ASN 146 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142D ARG* 2.8 39.9 + - - +
143D GLU* 4.0 4.5 - - - +
145D ILE* 1.3 73.0 - - - +
147D SER* 1.3 57.5 + - - +
149D VAL* 3.5 2.3 + - - +
150D GLU* 3.0 30.4 + - - +
157D ILE 4.8 0.9 - - - +
159D ASN* 3.7 21.1 + - - +
160D VAL* 3.3 15.7 + - - +
161D LEU* 2.8 55.0 + - - +
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Residues in contact with SER 147 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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183C LEU* 4.9 0.4 - - - +
190C ASP* 6.1 0.2 - - - -
337C ALA* 4.0 29.2 - - - +
338C GLY 4.4 8.0 + - - -
143D GLU* 2.9 21.3 + - - +
144D LEU* 2.8 22.9 + - - +
146D ASN* 1.3 75.6 - - - +
148D TRP* 1.3 58.6 + - - +
150D GLU* 3.9 6.9 - - - +
151D SER* 2.9 33.3 + - - -
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Residues in contact with TRP 148 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95C ASP* 2.9 31.5 + - + -
183C LEU* 4.5 17.0 - - + -
338C GLY 6.1 0.4 - - - +
102D ALA* 3.8 21.5 - - + -
103D SER 3.7 18.8 - - - -
104D ARG* 3.3 59.1 - - + +
106D TYR* 3.4 26.5 - + - +
127D GLY 4.9 1.3 - - - -
144D LEU 2.9 14.5 + - - +
145D ILE 3.1 2.0 + - - +
147D SER* 1.3 78.8 + - - +
149D VAL* 1.3 80.1 - - + +
151D SER* 3.9 2.9 - - - -
152D GLN* 3.0 54.5 + - + +
175D VAL* 4.0 7.2 - - + -
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Residues in contact with VAL 149 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102D ALA* 4.4 7.6 - - + -
145D ILE 3.1 15.3 + - - +
146D ASN 3.8 3.8 - - - +
148D TRP* 1.3 95.2 - - + +
150D GLU* 1.3 60.4 + - - +
152D GLN* 3.4 1.0 + - - +
153D THR* 2.9 29.7 + - + +
157D ILE* 3.8 30.5 - - + +
160D VAL* 3.9 24.7 - - + -
175D VAL* 4.1 19.3 - - + -
177D ALA* 3.8 19.1 - - + -
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Residues in contact with GLU 150 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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333C GLU* 5.6 0.5 - - - +
335C ASN* 5.1 9.9 + - - +
2401C SO4 4.6 10.7 + - - -
146D ASN 3.0 19.1 + - - +
147D SER* 3.9 6.6 - - - +
149D VAL* 1.3 75.3 - - - +
151D SER* 1.3 62.1 + - - +
153D THR* 3.3 6.0 + - - -
155D GLY* 2.7 46.5 + - - -
157D ILE 3.3 16.5 + - - +
158D ARG* 3.4 36.1 - - + +
159D ASN 4.9 1.2 + - - -
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Residues in contact with SER 151 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98C SER* 4.4 6.1 + - - -
181C LYS* 2.8 53.9 - - - +
182C GLY* 4.3 1.2 - - - -
183C LEU* 3.2 33.4 - - - +
337C ALA* 4.3 5.7 - - - +
147D SER 2.9 17.0 + - - -
148D TRP 3.9 0.4 - - - -
150D GLU* 1.3 79.7 - - - +
152D GLN* 1.3 62.2 + - - +
153D THR 3.4 0.5 + - - -
154D ASN* 3.5 7.6 + - - -
155D GLY 4.8 0.9 - - - +
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Residues in contact with GLN 152 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94C ASN 3.1 26.7 + - - +
95C ASP* 3.5 22.7 - - - +
96C VAL 3.9 3.3 + - - -
97C TYR* 3.9 15.2 + - - +
98C SER* 5.3 7.5 - - - -
183C LEU* 5.2 2.9 - - + +
100D SER* 4.1 14.6 - - - -
101D LEU 4.5 13.5 + - - +
102D ALA* 4.0 14.6 - - + +
148D TRP* 3.0 48.6 + - + +
149D VAL 3.8 3.8 - - - +
151D SER* 1.3 77.9 - - - +
153D THR* 1.3 57.8 + - - +
154D ASN* 3.4 4.6 + - - +
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Residues in contact with THR 153 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100D SER* 4.8 7.4 - - - +
102D ALA* 4.3 9.2 - - + -
149D VAL 2.9 19.2 + - - +
150D GLU 3.3 4.9 + - - -
152D GLN* 1.3 78.4 - - - +
154D ASN* 1.3 69.5 + - - +
156D ILE* 3.0 24.3 - - - +
157D ILE* 3.1 46.0 + - + +
177D ALA* 4.3 14.8 - - + +
179D VAL* 3.6 20.8 - - + +
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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