Contacts of the helix formed by residues 136 - 151 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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91C GLN* 4.8 22.7 + - - +
134C GLY 3.8 1.2 + - - -
135C THR* 1.3 72.9 - - - +
137C ALA* 1.3 57.5 + - - +
139C ARG* 3.3 23.0 + - - +
140C GLU* 2.9 53.0 + - - +
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Residues in contact with ALA 137 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105C ASN* 4.0 14.8 - - - +
135C THR* 3.3 4.1 - - - +
136C SER* 1.3 79.5 + - - +
138C ALA* 1.3 57.4 + - - +
141C ARG* 2.9 64.9 + - - +
164C PHE* 4.0 14.6 - - + -
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Residues in contact with ALA 138 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130C GLN* 5.2 2.2 - - + -
131C GLY* 3.9 16.6 - - - +
132C ILE 3.4 14.6 - - - +
133C ALA* 5.2 1.8 - - - -
134C GLY 5.5 0.4 - - - +
135C THR* 3.3 19.9 + - - +
137C ALA* 1.3 78.4 - - - +
139C ARG* 1.3 57.1 + - - +
142C GLY* 2.9 26.0 + - - -
164C PHE* 3.9 3.0 - - + -
189C GLN* 3.2 25.5 + - - +
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Residues in contact with ARG 139 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91C GLN* 4.9 7.9 + - - +
134C GLY 4.5 9.4 + - - -
135C THR 3.3 9.8 + - - +
136C SER* 3.7 27.5 - - - +
137C ALA 3.3 0.4 - - - -
138C ALA* 1.3 78.1 - - - +
140C GLU* 1.3 83.1 + - - +
142C GLY* 3.4 2.4 + - - -
143C GLU* 3.0 32.7 + - + +
260C LYS* 5.0 5.3 - - - +
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Residues in contact with GLU 140 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91C GLN* 4.6 6.8 - - - +
102C ALA* 6.0 1.2 - - - +
103C SER 4.4 3.8 - - - +
105C ASN* 3.4 37.1 + - + +
106C VAL* 3.4 24.8 + - + +
136C SER* 2.9 29.7 + - - +
139C ARG* 1.3 97.3 + - - +
141C ARG* 1.3 67.4 + - - +
143C GLU* 3.3 13.5 + - - +
144C GLY 3.0 18.5 + - - -
260C LYS* 4.6 6.6 + - - -
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Residues in contact with ARG 141 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105C ASN* 2.7 43.2 + - + +
109C GLY* 3.8 5.2 - - - -
137C ALA* 2.9 37.4 + - - +
140C GLU* 1.3 75.4 - - - +
142C GLY* 1.3 57.6 + - - +
144C GLY* 3.4 1.6 + - - -
145C PHE* 3.0 29.8 + - - +
164C PHE* 4.0 10.9 - - - -
187C PHE* 4.2 6.1 - - + -
189C GLN* 2.6 56.1 + - + -
190C ASN* 4.3 0.8 - - - +
214C PHE* 3.3 34.8 - - + -
215C ASP* 3.4 25.9 + - - -
235C GLN* 3.9 10.3 + - - +
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Residues in contact with GLY 142 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128C GLU* 3.8 6.9 - - - +
138C ALA 2.9 19.2 + - - -
139C ARG 3.7 1.8 - - - -
141C ARG* 1.3 76.7 - - - +
143C GLU* 1.3 60.1 + - - +
145C PHE* 3.4 3.6 + - - +
146C GLN* 3.1 28.3 + - - +
189C GLN* 3.6 14.5 - - - +
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Residues in contact with GLU 143 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106C VAL* 3.9 26.9 - - + +
139C ARG* 3.0 20.4 + - - +
140C GLU* 3.5 16.0 - - - +
142C GLY* 1.3 71.8 - - - +
144C GLY* 1.3 69.0 + - - +
146C GLN* 3.0 11.2 + - + +
147C GLN* 3.0 32.9 + - - +
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Residues in contact with GLY 144 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106C VAL* 3.0 37.2 - - - -
110C LYS* 3.2 22.1 - - - -
140C GLU 3.0 10.7 + - - -
141C ARG 3.8 2.7 - - - -
143C GLU* 1.3 78.7 - - - +
145C PHE* 1.3 61.1 + - - +
147C GLN* 3.1 16.5 + - - +
148C ALA 3.3 1.4 + - - -
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Residues in contact with PHE 145 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109C GLY 3.5 15.9 - - - +
113C GLY* 4.0 20.9 - - - -
116C ILE* 4.3 4.0 - - + -
126C VAL* 3.9 28.5 - - + -
127C ILE 5.3 0.4 - - - -
128C GLU* 3.5 46.2 - - + +
141C ARG 3.0 13.7 + - - +
142C GLY 3.7 1.6 - - - +
144C GLY* 1.3 73.5 - - - +
146C GLN* 1.3 61.5 + - - +
148C ALA* 3.1 5.1 + - - +
149C VAL* 2.8 45.5 + - + +
154C PHE* 4.2 9.0 - + - -
156C VAL* 4.5 4.7 - - + -
187C PHE* 3.5 38.1 - + + -
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Residues in contact with GLN 146 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128C GLU* 4.1 17.4 + - - -
142C GLY 3.1 17.0 + - - +
143C GLU* 3.0 14.1 + - + +
145C PHE* 1.3 74.6 - - - +
147C GLN* 1.3 64.4 + - - +
149C VAL* 3.1 28.1 + - - +
150C ALA* 3.0 24.8 + - - +
156C VAL* 4.8 9.0 - - - +
159C SER* 5.5 2.0 + - - -
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Residues in contact with GLN 147 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106C VAL* 3.4 29.4 - - - +
107C LEU* 6.0 0.2 - - - -
110C LYS* 3.6 29.3 - - + +
143C GLU* 3.0 25.2 + - + +
144C GLY* 3.1 7.6 + - - +
146C GLN* 1.3 76.2 - - - +
148C ALA* 1.3 57.2 + - - +
150C ALA* 3.4 5.2 + - - +
151C ALA* 3.0 30.7 + - - +
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Residues in contact with ALA 148 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110C LYS* 3.8 15.3 - - - +
113C GLY* 3.5 38.6 - - - -
114C ASP* 3.9 7.2 - - - +
144C GLY 3.3 5.3 + - - +
145C PHE 3.1 8.9 + - - +
147C GLN* 1.3 75.4 - - - +
149C VAL* 1.3 61.0 + - - +
151C ALA* 4.6 1.1 - - - -
152C HIS* 2.9 41.6 + - + +
154C PHE* 3.9 3.9 - - + -
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Residues in contact with VAL 149 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145C PHE* 2.8 50.5 + - + +
146C GLN* 3.1 25.5 + - - +
148C ALA* 1.3 76.5 - - - +
150C ALA* 1.3 57.6 + - - +
153C LYS* 2.9 9.7 + - - -
154C PHE* 2.9 51.8 + - + +
156C VAL* 3.7 19.7 - - + -
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Residues in contact with ALA 150 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146C GLN 3.0 12.5 + - - +
147C GLN* 3.7 8.3 - - - +
149C VAL* 1.3 75.8 - - - +
151C ALA* 1.3 66.8 + - - +
153C LYS* 3.2 18.7 + - - +
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Residues in contact with ALA 151 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110C LYS* 5.2 9.0 - - - +
122C GLU* 3.6 9.2 - - - +
147C GLN 3.0 17.6 + - - +
148C ALA* 4.2 2.9 - - - +
150C ALA* 1.3 76.7 - - - +
152C HIS* 1.3 74.8 + - + +
153C LYS* 3.6 7.4 + - - +
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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