Contacts of the helix formed by residues 304 - 311 (chain A) in PDB entry 1R1H
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 LEU 304 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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218A ILE* 5.7 2.0 - - + -
303A THR* 1.3 71.2 - - - +
305A ALA* 1.3 56.6 + - - +
307A ILE* 3.5 16.4 - - + +
308A GLN* 2.8 30.0 + - - +
322A TRP* 4.3 18.3 - - + +
323A LEU* 3.8 30.1 - - + +
326A THR* 4.0 20.0 - - + +
337A ILE* 3.6 29.4 - - + -
339A ASN* 3.5 21.6 + - - +
341A GLU* 2.9 15.8 + - + +
343A VAL* 3.8 24.0 - - + -
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Residues in contact with ALA 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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303A THR* 3.4 9.9 - - - +
304A LEU* 1.3 73.1 - - - +
306A GLN* 1.3 66.9 + - + +
308A GLN* 3.0 7.5 + - - +
309A ASN* 2.9 25.0 + - - +
339A ASN* 2.8 26.0 + - + +
340A GLU* 5.4 2.9 - - + -
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Residues in contact with GLN 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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301A LYS 4.5 4.0 + - - -
302A MET* 3.6 27.0 - - + +
303A THR* 2.9 46.1 + - + +
305A ALA* 1.3 73.4 - - + +
307A ILE* 1.3 51.5 + - - +
309A ASN* 3.0 6.0 + - - -
310A ASN* 2.7 53.6 + - - +
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Residues in contact with ILE 307 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
218A ILE* 4.6 6.5 - - + -
302A MET* 4.0 15.0 - - + -
303A THR 2.8 13.3 + - - +
304A LEU* 3.5 20.6 - - + +
306A GLN* 1.3 76.9 - - - +
308A GLN* 1.3 59.5 + - - +
311A PHE* 2.8 46.2 + - + +
322A TRP* 3.5 38.8 - - + -
343A VAL* 3.7 37.2 - - + -
345A VAL* 3.8 15.9 - - + -
351A LEU* 5.5 2.2 - - + -
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Residues in contact with GLN 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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304A LEU 2.8 20.3 + - - +
305A ALA* 3.5 7.6 - - - +
307A ILE* 1.3 74.0 - - - +
309A ASN* 1.3 66.6 + - - +
312A SER* 4.1 24.5 + - - +
319A PRO* 6.1 1.6 - - - +
320A PHE 2.9 21.5 + - - -
321A SER* 3.7 4.3 + - - +
322A TRP* 2.8 42.5 + - - +
323A LEU 4.3 2.1 + - - -
339A ASN* 4.8 7.2 + - - +
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Residues in contact with ASN 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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305A ALA 2.9 16.5 + - - +
306A GLN* 3.7 5.2 - - - +
308A GLN* 1.3 86.2 - - - +
310A ASN* 1.3 67.4 + - - +
312A SER* 5.2 2.9 + - - -
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Residues in contact with ASN 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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302A MET* 5.0 5.9 - - - +
306A GLN* 2.7 38.8 + - - +
309A ASN* 1.3 83.2 - - - +
311A PHE* 1.3 83.8 + - + +
312A SER 3.9 1.6 - - - -
352A THR* 4.9 1.6 + - - -
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Residues in contact with PHE 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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302A MET* 3.6 30.7 - - + -
307A ILE* 2.8 30.8 + - + +
308A GLN 4.4 0.2 - - - -
310A ASN* 1.3 99.9 - - + +
312A SER* 1.3 64.3 + - - +
313A LEU* 3.7 3.0 + - - +
322A TRP* 2.9 24.6 + - + -
345A VAL* 4.6 5.6 - - + -
348A PRO* 3.4 44.9 - - + -
351A LEU* 3.9 32.8 - - + -
352A THR* 3.5 20.4 - - - +
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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