Contacts of the helix formed by residues 298 - 311 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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93A ASN* 4.4 4.3 - - - +
95A TRP 6.0 0.2 - - - -
107A GLY 3.1 27.6 + - - +
108A GLU* 3.6 10.3 + - - -
109A GLU* 3.5 7.9 - - - +
110A HIS* 3.7 19.1 + - - +
157A ILE* 3.6 2.4 - - - +
161A ARG* 3.3 20.4 - - - +
164A ARG* 4.5 3.4 - - - +
297A GLY* 1.3 75.4 - - - -
299A GLN* 1.3 64.5 + - - +
300A SER* 2.8 15.2 + - - -
301A ASP* 2.7 43.9 + - - +
302A PHE* 3.0 18.2 + - - +
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Residues in contact with GLN 299 (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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93A ASN* 3.2 16.9 + - - +
109A GLU* 3.3 29.0 + - + +
136A LYS* 2.8 45.1 + - - +
137A TYR* 3.5 30.8 - - + -
298A ASN* 1.3 76.0 - - - +
300A SER* 1.3 62.0 + - - +
302A PHE* 3.5 14.6 + - - +
303A LEU* 3.1 26.2 + - - +
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Residues in contact with SER 300 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107A GLY 5.7 0.7 - - - -
160A TYR* 5.1 0.7 - - - -
298A ASN* 2.8 15.0 + - - -
299A GLN* 1.3 77.4 - - - +
301A ASP* 1.3 67.9 + - - +
303A LEU* 3.3 9.9 + - - +
304A GLY* 3.0 18.0 + - - -
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Residues in contact with ASP 301 (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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157A ILE* 3.7 20.1 - - + +
160A TYR* 4.0 21.1 - - + -
161A ARG* 2.9 38.2 + - - +
164A ARG* 2.9 31.4 + - - -
297A GLY* 4.2 0.4 - - - -
298A ASN* 2.7 32.5 + - - +
300A SER* 1.3 71.6 + - - +
302A PHE* 1.3 67.1 + - - +
304A GLY* 3.0 2.4 + - - -
305A ILE* 2.9 24.6 + - - +
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Residues in contact with PHE 302 (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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91A ALA 4.1 11.4 - - - -
92A VAL 3.9 3.8 - - - -
93A ASN* 3.5 43.1 - - + +
137A TYR 3.7 15.7 - - - -
138A MET 4.3 2.5 - - - -
139A TYR* 3.7 25.1 - + + -
152A LEU 4.8 0.2 - - - -
153A THR* 3.9 20.9 - - + -
157A ILE* 3.5 25.0 - - + +
298A ASN 3.0 8.7 + - - +
299A GLN* 3.6 16.8 - - - +
301A ASP* 1.3 76.7 - - - +
303A LEU* 1.3 66.6 + - + +
305A ILE* 3.3 7.0 - - + +
306A MET* 3.0 50.3 + - + +
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Residues in contact with LEU 303 (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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139A TYR* 4.3 23.8 - - + -
299A GLN 3.1 12.0 + - - +
300A SER* 3.4 13.2 - - - +
302A PHE* 1.3 83.0 - - + +
304A GLY* 1.3 62.9 + - - +
306A MET* 3.5 3.8 + - - +
307A ARG* 3.1 36.3 + - + +
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Residues in contact with GLY 304 (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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160A TYR* 3.5 27.4 + - - -
300A SER 3.0 10.0 + - - -
301A ASP 3.0 8.0 + - - -
303A LEU* 1.3 79.0 - - - +
305A ILE* 1.3 60.2 + - - +
307A ARG* 4.1 3.1 - - - +
308A LEU* 3.1 24.1 + - - +
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Residues in contact with ILE 305 (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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152A LEU* 3.9 27.4 - - + +
156A GLY* 3.7 22.4 - - - +
157A ILE* 4.0 6.7 - - + +
160A TYR* 3.8 13.9 - - + -
186A MET* 4.1 12.6 - - + -
190A ILE* 3.5 36.8 - - + -
301A ASP 2.9 17.1 + - - +
302A PHE* 3.3 17.5 - - + +
304A GLY* 1.3 69.9 - - - -
306A MET* 1.3 76.4 + - + +
308A LEU* 3.4 2.8 + - + +
309A ALA* 3.0 22.7 + - - +
314A VAL* 4.2 8.1 - - + -
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Residues in contact with MET 306 (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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91A ALA* 3.5 21.5 - - + -
139A TYR* 3.7 33.4 - - + -
141A LEU* 3.5 32.3 - - + -
144A LEU* 4.6 2.9 - - + -
149A ALA* 4.8 0.2 - - + -
152A LEU* 3.8 37.5 - - + -
302A PHE* 3.0 45.9 + - + +
303A LEU 4.0 0.2 - - - +
305A ILE* 1.3 79.6 - - + +
307A ARG* 1.3 57.3 + - - +
309A ALA* 3.8 2.7 - - - +
310A GLU* 2.9 35.3 + - - +
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Residues in contact with ARG 307 (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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139A TYR* 3.3 27.1 - - + +
303A LEU* 3.1 27.6 + - + +
304A GLY* 4.1 3.8 - - - +
306A MET* 1.3 73.9 - - - +
308A LEU* 1.3 66.4 + - - +
310A GLU* 3.9 4.5 - - - +
311A ALA* 3.1 24.8 + - - +
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Residues in contact with LEU 308 (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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160A TYR* 4.5 8.5 - - + -
190A ILE* 4.2 25.1 - - + -
193A ALA* 4.4 1.6 - - + -
194A VAL* 3.7 28.0 - - + -
304A GLY 3.1 18.1 + - - +
305A ILE* 3.7 9.6 - - + +
307A ARG* 1.3 79.1 - - - +
309A ALA* 1.3 58.8 + - - +
311A ALA* 3.4 5.3 + - - +
313A LYS* 3.0 57.9 + - + +
314A VAL* 3.6 32.3 - - + -
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Residues in contact with ALA 309 (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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143A ARG* 4.2 1.2 + - - -
144A LEU* 3.7 21.3 - - + +
152A LEU* 3.6 31.2 - - + -
305A ILE 3.0 17.1 + - - +
306A MET 3.9 1.1 - - - +
308A LEU* 1.3 74.2 - - - +
310A GLU* 1.3 59.1 + - - +
311A ALA 3.1 2.0 - - - -
312A GLY* 2.8 19.9 + - - -
314A VAL* 3.6 26.9 - - + +
316A PRO* 5.5 1.6 - - + -
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Residues in contact with GLU 310 (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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139A TYR* 3.9 28.1 + - + +
140A LYS 4.2 0.5 - - - +
141A LEU* 4.0 4.3 - - - +
142A ARG* 3.0 36.6 + - - +
143A ARG* 3.1 43.7 + - + +
144A LEU* 3.1 31.1 + - + +
306A MET* 2.9 25.9 + - + +
307A ARG* 3.9 7.4 - - - +
309A ALA* 1.3 77.5 - - - +
311A ALA* 1.3 59.2 + - - +
312A GLY 3.1 0.9 + - - -
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Residues in contact with ALA 311 (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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143A ARG* 4.4 2.6 + - - -
307A ARG 3.1 18.1 + - - +
308A LEU* 3.6 6.5 - - - +
309A ALA 3.1 0.8 - - - -
310A GLU* 1.3 75.1 - - - +
312A GLY* 1.3 62.1 + - - +
313A LYS* 3.4 28.3 + - + +
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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