Contacts of the helix formed by residues 298 - 311 (chain B) in PDB entry 1R37
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 ASN 298 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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93B ASN* 4.4 4.5 - - - +
95B TRP 6.0 0.2 - - - -
107B GLY 3.1 27.1 + - - +
108B GLU* 3.5 12.0 + - - -
109B GLU* 3.7 9.2 - - - +
110B HIS* 3.7 16.1 + - - +
157B ILE* 3.6 3.1 - - - +
161B ARG* 3.4 18.6 - - - +
164B ARG* 4.5 4.2 - - - +
297B GLY* 1.3 74.5 - - - -
299B GLN* 1.3 65.9 + - - +
300B SER* 2.9 15.0 + - - -
301B ASP* 2.7 45.7 + - - +
302B PHE* 3.0 19.2 + - - +
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Residues in contact with GLN 299 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93B ASN* 3.2 18.8 + - - +
109B GLU* 3.5 34.6 + - + +
136B LYS* 2.9 43.0 + - - +
137B TYR* 3.4 25.2 - - + -
298B ASN* 1.3 76.2 - - - +
300B SER* 1.3 60.3 + - - +
302B PHE* 3.6 14.0 - - - +
303B LEU* 3.1 26.2 + - - +
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Residues in contact with SER 300 (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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107B GLY 5.7 0.4 - - - -
109B GLU* 4.9 0.2 + - - -
160B TYR* 5.1 1.1 - - - -
164B ARG* 6.3 0.2 - - - -
298B ASN* 2.9 15.1 + - - -
299B GLN* 1.3 77.4 - - - +
301B ASP* 1.3 62.4 + - - +
303B LEU* 3.4 11.0 + - - +
304B GLY* 3.0 23.7 + - - -
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Residues in contact with ASP 301 (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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157B ILE* 3.6 19.5 - - + +
160B TYR* 4.0 21.2 - - + -
161B ARG* 2.9 30.5 + - - +
164B ARG* 3.0 31.7 + - - -
297B GLY* 3.4 4.3 - - - -
298B ASN* 2.7 37.6 + - - +
300B SER* 1.3 70.5 + - - +
302B PHE* 1.3 67.7 + - - +
304B GLY* 3.0 2.8 + - - -
305B ILE* 2.9 24.6 + - - +
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Residues in contact with PHE 302 (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 ALA 4.0 11.4 - - - -
92B VAL 3.9 3.6 - - - -
93B ASN* 3.5 44.9 - - + +
137B TYR 3.7 15.7 - - - -
138B MET 4.2 3.4 - - - -
139B TYR* 3.7 24.7 - + + -
152B LEU 4.8 0.9 - - - -
153B THR* 4.0 16.8 - - + -
157B ILE* 3.5 21.4 - - + +
298B ASN 3.0 12.1 + - - +
299B GLN* 3.6 17.7 - - - +
301B ASP* 1.3 76.2 - - - +
303B LEU* 1.3 68.8 + - + +
305B ILE* 3.2 9.6 - - + +
306B MET* 2.9 50.3 + - + +
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Residues in contact with LEU 303 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139B TYR* 4.4 23.3 - - + -
299B GLN 3.1 12.0 + - - +
300B SER* 3.4 13.0 - - - +
302B PHE* 1.3 83.1 - - + +
304B GLY* 1.3 62.9 + - - +
306B MET* 4.0 3.7 - - - +
307B ARG* 3.1 35.9 + - + +
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Residues in contact with GLY 304 (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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160B TYR* 3.6 28.2 + - - -
300B SER 3.0 10.7 + - - -
301B ASP 3.0 8.2 + - - -
303B LEU* 1.3 77.4 - - - +
305B ILE* 1.3 60.8 + - - +
307B ARG* 4.1 3.1 - - - +
308B LEU* 3.2 23.7 + - - +
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Residues in contact with ILE 305 (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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152B LEU* 3.8 31.2 - - + +
156B GLY* 3.7 18.6 - - - +
157B ILE* 4.0 7.6 - - + +
160B TYR* 3.8 13.9 - - + -
186B MET* 4.1 14.6 - - + -
190B ILE* 3.6 33.2 - - + -
301B ASP 2.9 16.3 + - - +
302B PHE* 3.2 17.5 - - + +
304B GLY* 1.3 70.3 - - - +
306B MET* 1.3 75.7 + - + +
308B LEU* 3.3 3.0 + - + -
309B ALA* 3.0 22.2 + - - +
314B VAL* 4.1 8.7 - - + -
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Residues in contact with MET 306 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91B ALA* 3.5 26.2 - - + -
139B TYR* 3.8 36.8 - - + -
141B LEU* 3.7 19.5 - - + -
144B LEU* 4.5 4.7 - - + -
149B ALA* 4.8 1.1 - - + -
152B LEU* 3.9 37.9 - - + -
302B PHE* 2.9 48.5 + - + +
303B LEU 4.0 0.9 - - - +
305B ILE* 1.3 81.1 - - - +
307B ARG* 1.3 58.1 + - - +
309B ALA* 3.8 1.4 - - - +
310B GLU* 2.9 35.0 + - - +
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Residues in contact with ARG 307 (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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139B TYR* 3.3 27.4 - - + +
303B LEU* 3.1 25.4 + - + +
304B GLY* 4.1 4.3 - - - +
306B MET* 1.3 73.9 - - - +
308B LEU* 1.3 63.8 + - - +
310B GLU* 3.9 5.0 - - - +
311B ALA* 3.1 25.1 + - - +
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Residues in contact with LEU 308 (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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160B TYR* 4.5 11.7 - - + -
190B ILE* 4.2 23.3 - - + -
193B ALA* 4.5 1.3 - - + -
194B VAL* 3.7 29.6 - - + -
304B GLY 3.2 18.0 + - - +
305B ILE* 3.7 7.6 - - + +
306B MET 3.3 0.2 - - - -
307B ARG* 1.3 78.6 - - - +
309B ALA* 1.3 58.2 + - - +
311B ALA* 3.5 5.8 + - - +
313B LYS* 3.0 58.8 + - + +
314B VAL* 3.7 29.4 - - + -
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Residues in contact with ALA 309 (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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143B ARG* 4.2 1.2 + - - -
144B LEU* 3.7 22.6 - - + +
152B LEU* 3.5 35.0 - - + -
305B ILE 3.0 12.1 + - - +
306B MET 3.9 0.7 - - - +
308B LEU* 1.3 74.0 - - - +
310B GLU* 1.3 60.1 + - - +
311B ALA 3.1 1.6 - - - -
312B GLY* 2.9 19.6 + - - -
314B VAL* 3.5 27.5 - - + +
316B PRO* 5.5 1.8 - - + -
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Residues in contact with GLU 310 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139B TYR* 3.9 28.5 + - + +
141B LEU* 3.9 3.5 - - - -
142B ARG* 2.8 38.3 + - - +
143B ARG* 3.1 29.4 + - + +
144B LEU* 3.0 46.4 + - + +
306B MET* 2.9 25.5 + - - +
307B ARG* 3.9 8.7 - - - +
308B LEU 3.5 0.2 - - - -
309B ALA* 1.3 76.6 - - - +
311B ALA* 1.3 60.1 + - - +
312B GLY 3.3 1.0 + - - -
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Residues in contact with ALA 311 (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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143B ARG* 4.5 2.6 + - - -
307B ARG 3.1 18.7 + - - +
308B LEU 3.7 5.8 - - - +
309B ALA 3.1 0.6 - - - -
310B GLU* 1.3 76.0 - - - +
312B GLY* 1.3 61.7 + - - +
313B LYS* 3.4 28.6 + - + +
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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