Contacts of the helix formed by residues 136 - 151 (chain B) in PDB entry 1URP
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 SER 136 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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89B ASP 5.7 0.7 + - - -
90B ARG* 6.1 0.3 - - - -
91B GLN* 5.0 20.9 + - - +
105B ASN* 5.1 0.2 - - - -
134B GLY 3.8 1.4 + - - -
135B THR* 1.3 73.1 - - - +
137B ALA* 1.3 58.1 + - - +
139B ARG* 3.4 24.4 + - - +
140B GLU* 3.0 51.8 + - - +
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Residues in contact with ALA 137 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105B ASN* 4.0 14.6 - - - +
135B THR* 3.3 3.9 - - - +
136B SER* 1.3 80.3 + - - +
138B ALA* 1.3 57.6 + - - +
140B GLU* 4.2 0.2 - - - +
141B ARG* 2.9 65.3 + - - +
164B PHE* 4.0 13.9 - - + -
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Residues in contact with ALA 138 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130B GLN* 5.2 2.6 - - + +
131B GLY* 3.9 16.4 - - - +
132B ILE 3.4 14.4 - - - +
133B ALA* 5.2 1.8 - - - -
134B GLY 5.4 0.7 - - - +
135B THR* 3.2 20.6 + - - +
137B ALA* 1.3 77.8 - - - +
139B ARG* 1.3 56.3 + - - +
142B GLY* 3.0 23.6 + - - -
164B PHE* 3.9 3.4 - - + -
189B GLN* 3.2 28.0 + - - +
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Residues in contact with ARG 139 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91B GLN* 5.0 7.5 + - - +
134B GLY 4.5 9.8 + - - +
135B THR 3.3 11.4 + - - +
136B SER* 3.7 26.0 - - - +
137B ALA 3.3 0.6 - - - -
138B ALA* 1.3 79.5 - - - +
140B GLU* 1.3 81.0 + - - +
142B GLY* 3.3 2.1 + - - -
143B GLU* 2.9 35.1 + - + +
260B LYS* 5.1 4.8 - - - +
143D GLU* 3.0 46.7 + - + +
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Residues in contact with GLU 140 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91B GLN* 4.8 1.9 - - - +
102B ALA* 5.9 1.2 - - - +
103B SER 4.3 6.2 - - - +
105B ASN* 3.4 34.0 + - + +
106B VAL* 3.4 24.6 + - + +
136B SER* 3.0 28.5 + - - +
139B ARG* 1.3 96.3 + - - +
141B ARG* 1.3 66.4 + - - +
143B GLU* 3.3 13.7 + - - +
144B GLY 3.0 19.1 + - - -
260B LYS* 4.6 10.9 + - - -
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Residues in contact with ARG 141 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105B ASN* 2.7 42.8 + - + +
109B GLY* 3.7 4.4 - - - -
137B ALA* 2.9 38.0 + - - +
140B GLU* 1.3 75.0 - - - +
142B GLY* 1.3 57.1 + - - +
144B GLY* 3.3 1.7 + - - -
145B PHE* 3.0 30.1 + - - +
164B PHE* 4.1 9.9 - - - -
187B PHE* 4.2 6.0 - - + -
189B GLN* 2.7 56.3 + - + -
190B ASN* 4.3 1.0 - - - +
214B PHE* 3.3 35.2 - - + -
215B ASP* 3.4 26.7 + - - -
235B GLN* 3.8 10.7 - - - +
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Residues in contact with GLY 142 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128B GLU* 3.9 8.2 - - - +
138B ALA 3.0 20.2 + - - -
139B ARG 3.6 1.3 - - - -
141B ARG* 1.3 76.5 - - - +
143B GLU* 1.3 61.2 + - - +
145B PHE* 3.4 3.8 + - - +
146B GLN* 3.0 28.4 + - - +
189B GLN* 3.6 13.6 - - - +
146D GLN* 6.5 0.4 - - - -
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Residues in contact with GLU 143 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106B VAL* 3.9 25.6 - - + +
139B ARG* 2.9 23.0 + - + +
140B GLU* 3.5 17.0 - - - +
142B GLY* 1.3 72.0 - - - +
144B GLY* 1.3 67.6 + - - +
146B GLN* 3.1 11.8 + - + +
147B GLN* 3.0 33.3 + - + +
139D ARG* 3.0 45.0 + - + +
143D GLU* 6.4 1.8 - - + -
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Residues in contact with GLY 144 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106B VAL* 3.0 36.8 - - - -
110B LYS* 3.2 21.9 - - - -
140B GLU 3.0 10.9 + - - -
141B ARG 3.7 2.9 - - - -
143B GLU* 1.3 79.2 - - - +
145B PHE* 1.3 60.7 + - - +
147B GLN* 3.1 17.9 + - - +
148B ALA 3.4 1.0 + - - -
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Residues in contact with PHE 145 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109B GLY 3.5 15.9 - - - +
113B GLY* 4.0 20.6 - - - -
116B ILE* 4.3 4.3 - - + -
126B VAL* 3.9 29.4 - - + -
127B ILE 5.4 0.4 - - - -
128B GLU* 3.5 44.9 - - + +
141B ARG 3.0 13.8 + - - +
142B GLY 3.7 1.8 - - - +
143B GLU 3.3 0.2 - - - -
144B GLY* 1.3 74.1 - - - +
146B GLN* 1.3 60.1 + - - +
148B ALA* 3.0 5.8 + - - +
149B VAL* 2.8 46.9 + - + +
154B PHE* 4.1 10.1 - + - -
156B VAL* 4.4 4.7 - - + -
187B PHE* 3.6 38.6 - + + -
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Residues in contact with GLN 146 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128B GLU* 4.2 15.6 + - - -
142B GLY 3.0 17.8 + - - +
143B GLU* 3.1 12.7 + - + +
145B PHE* 1.3 77.2 - - - +
147B GLN* 1.3 62.7 + - - +
149B VAL* 3.4 29.0 - - - +
150B ALA* 2.9 25.1 + - - +
156B VAL* 4.8 9.1 - - - +
128D GLU* 5.1 0.3 - - - +
130D GLN* 4.6 12.4 + - - +
142D GLY 6.4 0.9 - - - -
146D GLN* 3.8 43.3 + - + +
156D VAL* 6.0 0.3 - - - +
159D SER* 4.1 13.7 + - - -
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Residues in contact with GLN 147 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106B VAL* 3.4 29.4 - - - +
107B LEU* 6.0 0.2 - - - -
110B LYS* 3.6 29.7 - - + +
143B GLU* 3.0 26.9 + - - +
144B GLY* 3.1 7.4 + - - +
146B GLN* 1.3 76.4 - - - +
148B ALA* 1.3 56.5 + - - +
150B ALA* 3.4 5.2 + - - +
151B ALA* 3.0 29.9 + - - +
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Residues in contact with ALA 148 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110B LYS* 3.8 18.2 - - - +
113B GLY* 3.5 38.6 - - - -
114B ASP* 3.9 6.7 - - - +
144B GLY 3.4 2.0 + - - -
145B PHE 3.0 8.7 + - - +
147B GLN* 1.3 74.2 - - - +
149B VAL* 1.3 60.2 + - - +
151B ALA* 4.5 1.6 - - - +
152B HIS* 2.8 40.9 + - + +
154B PHE* 3.9 4.1 - - + -
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Residues in contact with VAL 149 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145B PHE* 2.8 50.1 + - + +
146B GLN* 3.1 25.5 + - - +
148B ALA* 1.3 75.9 - - - +
150B ALA* 1.3 56.8 + - - +
153B LYS* 2.9 9.7 + - - -
154B PHE* 2.9 53.0 + - + +
156B VAL* 3.7 20.2 - - + -
156D VAL* 6.0 1.1 - - + -
159D SER* 4.2 19.2 + - - +
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Residues in contact with ALA 150 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146B GLN 2.9 12.0 + - - +
147B GLN* 3.7 8.7 - - - +
149B VAL* 1.3 74.5 - - - +
151B ALA* 1.3 67.8 + - - +
153B LYS* 3.2 10.9 + - - +
130D GLN* 4.2 17.5 - - - +
159D SER 3.3 21.1 + - - +
160D GLN* 3.6 18.4 + - - +
161D PRO* 4.2 13.9 - - + -
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Residues in contact with ALA 151 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110B LYS* 5.2 8.7 - - - +
122B GLU* 3.6 9.7 - - - +
147B GLN 3.0 15.5 + - - +
148B ALA* 4.5 0.9 - - - -
150B ALA* 1.3 80.1 - - - +
152B HIS* 1.3 76.2 + - + +
153B LYS* 3.7 6.8 + - - +
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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