Contacts of the helix formed by residues 298 - 307 (chain A) in PDB entry 3RSS
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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287A ILE* 3.1 26.8 - - + +
288A ASP 3.0 25.9 + - - +
289A THR* 3.8 8.5 - - - +
293A PHE 4.2 0.2 - - - +
294A PHE* 3.6 22.2 - - + -
295A SER* 2.8 33.8 + - - +
297A GLN* 1.3 86.1 + - - +
299A LEU* 1.3 64.6 + - - +
300A GLN 3.4 1.8 - - - -
301A GLU* 3.4 13.1 + - + +
302A CYS* 3.1 23.8 + - - -
327A PHE* 4.0 2.5 - - + -
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Residues in contact with LEU 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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295A SER 3.9 1.2 + - - -
296A LEU* 3.0 29.4 + - + +
297A GLN 3.4 0.4 - - - -
298A ASN* 1.3 76.4 - - - +
300A GLN* 1.3 65.3 + - - +
302A CYS* 3.2 4.3 + - - +
303A LEU* 3.0 46.9 + - + +
327A PHE* 4.1 11.0 - - + +
330A GLU* 4.1 24.7 - - + +
331A PHE* 3.7 39.0 - - + +
334A THR* 5.5 2.5 - - - +
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Residues in contact with GLN 300 (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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296A LEU 4.8 0.2 + - - -
297A GLN 4.9 3.0 + - - +
298A ASN 3.4 0.6 - - - -
299A LEU* 1.3 80.9 - - - +
301A GLU* 1.3 64.8 + - - +
303A LEU* 3.3 20.0 + - - +
304A GLU* 3.0 39.3 + - + +
307A LYS* 4.4 5.7 - - - +
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Residues in contact with GLU 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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285A VAL* 4.4 8.5 - - - +
286A PRO 4.3 7.4 - - - +
287A ILE* 3.8 39.0 - - + +
288A ASP 5.0 2.3 + - - -
297A GLN 5.4 1.0 + - - +
298A ASN* 3.4 14.5 + - - +
299A LEU 3.3 0.4 - - - -
300A GLN* 1.3 79.3 - - - +
302A CYS* 1.3 58.5 + - - +
304A GLU* 3.4 7.9 + - + +
305A LEU* 3.0 34.8 + - + +
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Residues in contact with CYS 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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236A LEU* 4.0 1.8 - - - +
238A ILE* 4.0 15.5 - - + -
266A ALA* 4.8 8.5 - - - -
287A ILE* 4.8 5.8 - - - -
294A PHE* 3.7 29.6 - - - -
298A ASN* 3.1 22.3 + - - +
299A LEU 3.8 3.1 - - - +
301A GLU* 1.3 74.4 - - - +
303A LEU* 1.3 60.9 + - - +
305A LEU* 3.3 7.8 + - - +
306A SER* 3.0 31.7 + - - -
327A PHE* 3.8 12.8 - - + -
331A PHE* 3.8 20.2 - - + -
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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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299A LEU* 3.0 44.1 + - + +
300A GLN* 3.8 19.7 - - - +
302A CYS* 1.3 76.0 - - - +
304A GLU* 1.3 62.7 + - - +
306A SER* 3.2 13.9 + - - -
307A LYS* 3.3 21.7 + - - +
331A PHE* 3.7 25.6 - - + +
334A THR* 3.7 39.5 - - + +
335A LEU* 4.1 16.2 - - + +
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Residues in contact with GLU 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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300A GLN* 3.0 24.6 + - + +
301A GLU* 3.5 11.9 - - + +
303A LEU* 1.3 76.5 - - - +
305A LEU* 1.3 63.8 + - + +
307A LYS* 2.9 50.1 + - - +
308A ASP* 3.8 8.7 - - - +
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Residues in contact with LEU 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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236A LEU* 4.0 18.1 - - + +
264A LYS* 5.1 18.5 + - + +
266A ALA* 4.1 26.2 - - + -
285A VAL* 4.3 31.4 - - + -
287A ILE* 4.4 2.5 - - + -
301A GLU* 3.0 34.1 + - + +
302A CYS* 3.3 8.0 + - - +
304A GLU* 1.3 77.4 - - + +
306A SER* 1.3 61.5 + - - +
307A LYS 3.4 0.7 + - - -
308A ASP* 3.6 13.3 + - - +
309A VAL* 3.8 15.6 - - - +
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Residues in contact with SER 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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236A LEU* 3.5 9.3 - - - +
302A CYS 3.0 14.5 + - - -
303A LEU* 3.2 12.3 + - - -
305A LEU* 1.3 74.8 - - - +
307A LYS* 1.3 55.2 + - - +
308A ASP 3.2 1.1 + - - -
309A VAL* 3.3 19.1 + - - +
312A VAL* 3.5 4.2 - - - +
331A PHE* 3.4 20.3 - - - -
335A LEU* 3.5 24.7 - - - +
337A LYS* 2.7 28.2 + - - +
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Residues in contact with LYS 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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300A GLN* 4.4 8.3 - - - +
303A LEU* 3.6 13.5 + - - +
304A GLU* 2.9 49.1 + - - +
305A LEU 3.3 1.4 - - - -
306A SER* 1.3 78.1 - - - +
308A ASP* 1.3 65.3 + - - +
309A VAL 4.2 0.3 - - - +
337A LYS* 3.2 16.0 + - - +
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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