Contacts of the helix formed by residues 321 - 331 (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 SER 321 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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184A GLU* 3.9 8.9 + - - +
308A GLN* 3.7 5.6 + - - -
318A LYS* 5.0 6.1 - - - -
319A PRO 3.8 4.3 + - - -
320A PHE* 1.3 75.1 - - - +
322A TRP* 1.3 60.1 + - - +
323A LEU* 3.8 8.1 + - - +
324A ASN* 3.1 28.9 + - - +
325A PHE* 2.8 30.3 + - - +
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Residues in contact with TRP 322 (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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200A ILE* 3.9 21.3 - - + -
218A ILE* 3.7 31.6 - - + -
304A LEU* 4.3 17.3 - - + +
307A ILE* 3.5 30.4 - - + +
308A GLN* 2.8 41.5 + - - +
311A PHE 2.9 26.3 + - - -
312A SER* 4.7 1.8 - - - +
313A LEU* 4.0 17.0 - - + +
320A PHE* 3.7 22.4 - + - -
321A SER* 1.3 68.6 - - - +
323A LEU* 1.3 61.0 + - - +
325A PHE* 3.9 13.6 - + - +
326A THR* 2.9 39.4 + - - -
351A LEU* 3.8 31.9 - - + -
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Residues in contact with LEU 323 (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* 3.8 13.7 - - + +
308A GLN* 4.3 2.2 + - - +
321A SER* 3.3 7.8 - - - +
322A TRP* 1.3 79.8 - - - +
324A ASN* 1.3 55.3 + - - +
326A THR* 3.9 0.3 - - - -
327A ASN* 2.9 48.3 + - - +
337A ILE* 3.3 18.2 - - + +
339A ASN* 2.3 72.4 - - + +
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Residues in contact with ASN 324 (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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184A GLU* 3.4 25.1 - - - +
185A LYS* 5.3 0.2 - - - +
318A LYS* 4.6 1.9 + - - -
321A SER* 3.1 25.3 + - - +
323A LEU* 1.3 77.7 - - - +
325A PHE* 1.3 56.2 + - - +
327A ASN* 3.3 3.2 + - - +
328A GLU* 2.7 41.5 + - - +
753A NAG 1.4 71.6 + - - +
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Residues in contact with PHE 325 (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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184A GLU* 3.7 27.8 - - + +
187A ILE* 3.5 33.7 - - + -
188A ALA* 4.1 3.1 - - + -
191A ASN* 5.3 0.7 - - - -
200A ILE* 4.2 24.0 - - + -
202A LEU* 4.1 22.9 - - + -
218A ILE* 4.7 1.3 - - + -
320A PHE* 3.5 29.4 - + + -
321A SER 2.8 19.2 + - - +
322A TRP* 3.9 19.7 - + - +
324A ASN* 1.3 74.6 + - - +
326A THR* 1.3 65.6 + - - +
328A GLU* 3.2 3.6 + - - +
329A ILE* 3.1 46.0 + - + +
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Residues in contact with THR 326 (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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202A LEU* 5.1 8.7 - - + +
216A ILE* 4.0 21.4 - - + +
218A ILE* 5.2 2.8 - - - +
304A LEU* 4.0 18.7 - - + +
322A TRP* 2.9 26.7 + - - -
323A LEU 3.9 2.5 - - - -
325A PHE* 1.3 83.9 - - - +
327A ASN* 1.3 61.8 + - - +
329A ILE* 3.4 8.5 + - - +
330A MET* 2.9 28.4 + - + +
337A ILE* 3.6 30.1 - - + -
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Residues in contact with ASN 327 (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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323A LEU* 2.9 34.5 + - - +
324A ASN* 4.0 1.5 - - - +
326A THR* 1.3 72.9 - - - +
328A GLU* 1.3 59.7 + - - +
329A ILE 3.1 2.2 - - - -
330A MET 4.2 0.9 - - - +
331A SER* 2.6 39.0 + - - +
335A ILE 4.1 2.3 - - - +
336A SER* 3.8 5.4 - - - -
337A ILE* 2.8 52.0 + - - +
753A NAG 3.9 19.9 + - + +
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Residues in contact with GLU 328 (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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184A GLU 4.7 2.2 - - - +
185A LYS* 3.9 31.2 - - + +
188A ALA* 3.9 17.6 - - + +
192A SER* 4.5 3.3 + - - -
324A ASN* 2.7 29.9 + - - +
325A PHE* 3.6 6.5 - - - +
327A ASN* 1.3 72.9 - - - +
329A ILE* 1.3 60.7 + - - +
331A SER* 3.7 9.9 + - - -
332A THR* 4.4 5.2 + - - -
753A NAG 2.8 53.9 + - - +
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Residues in contact with ILE 329 (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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188A ALA* 3.5 24.5 - - + +
191A ASN* 3.9 28.5 - - + +
192A SER* 3.9 6.1 - - - -
202A LEU* 4.0 18.4 - - + -
325A PHE* 3.1 42.0 + - + +
326A THR* 3.5 7.6 - - - +
328A GLU* 1.3 77.6 - - - +
330A MET* 1.3 69.5 + - + +
332A THR* 2.9 32.4 + - - -
522A LEU* 4.1 28.5 - - + +
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Residues in contact with MET 330 (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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202A LEU* 5.4 2.9 - - + -
204A VAL* 4.3 9.0 - - - -
216A ILE* 4.2 13.2 - - + -
326A THR* 2.9 24.5 + - + +
327A ASN 4.3 0.4 - - - +
329A ILE* 1.3 73.4 - - + +
331A SER* 1.3 55.3 + - - +
332A THR 2.7 15.5 + - - -
333A VAL* 3.0 12.4 + - + +
335A ILE* 3.2 56.7 + - + +
337A ILE* 3.7 22.4 - - + -
522A LEU* 3.8 48.9 - - + +
525A LEU* 4.0 10.1 - - + -
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Residues in contact with SER 331 (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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327A ASN* 2.6 26.3 + - - -
328A GLU* 3.7 13.7 + - - -
330A MET* 1.3 71.5 - - - +
332A THR* 1.3 59.6 + - - +
333A VAL 3.2 0.4 - - - -
334A ASN* 3.1 19.2 + - - +
335A ILE 3.6 10.8 + - - +
753A NAG 4.6 10.7 - - - +
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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