Contacts of the helix formed by residues 297 - 305 (chain A) in PDB entry 4B18
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 VAL 297 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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260A SER* 3.3 40.2 - - - +
263A LEU* 3.6 18.8 - - + -
278A LEU* 3.9 15.7 - - + -
292A VAL* 3.4 35.3 + - + +
293A ILE 4.3 0.2 + - - -
295A ALA* 4.2 4.9 - - + +
296A GLY* 1.3 75.3 - - - +
298A CYS* 1.3 68.9 + - - +
299A ARG 3.3 0.9 - - - -
300A ARG* 3.1 6.5 + - - +
301A LEU* 2.8 39.9 + - + +
323A ILE* 5.1 1.1 - - + -
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Residues in contact with CYS 298 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
293A ILE* 4.0 28.0 - - - -
296A GLY* 3.3 3.0 - - - -
297A VAL* 1.3 77.8 - - - +
299A ARG* 1.3 58.8 + - - +
301A LEU* 3.1 8.5 + - - +
302A VAL* 2.7 33.8 + - - +
323A ILE* 4.2 9.9 - - - -
333A VAL* 3.9 24.5 - - + -
334A ILE* 3.6 26.0 - - + -
337A CYS* 3.9 16.6 - - - -
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Residues in contact with ARG 299 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
296A GLY 4.4 5.1 + - - +
297A VAL 3.3 0.4 - - - -
298A CYS* 1.3 78.9 - - - +
300A ARG* 1.3 66.2 + - - +
302A VAL* 3.3 1.6 + - - +
303A GLU* 2.9 52.2 + - + +
336A ASN 3.4 23.4 + - - -
337A CYS* 3.7 39.2 + - + +
338A SER* 5.4 2.0 + - - -
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Residues in contact with ARG 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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260A SER 5.3 0.2 - - - +
263A LEU* 3.1 50.8 + - + -
264A PHE* 3.5 52.2 + - + +
265A VAL 4.8 5.7 + - - -
271A LEU* 5.0 2.0 - - - +
296A GLY 5.0 1.6 + - - +
297A VAL* 3.1 6.7 + - - +
299A ARG* 1.3 77.0 - - - +
301A LEU* 1.3 59.4 + - - +
303A GLU* 2.8 40.3 + - - +
304A LEU* 2.8 58.2 + - + +
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Residues in contact with LEU 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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263A LEU* 4.0 12.8 - - + -
275A CYS* 3.8 28.7 - - + -
278A LEU* 4.3 10.3 - - + -
292A VAL* 5.2 0.2 - - + -
297A VAL* 2.8 42.8 + - + +
298A CYS* 3.3 5.2 - - - +
300A ARG* 1.3 78.3 - - - +
302A VAL* 1.3 62.6 + - - +
304A LEU* 3.2 14.9 + - - +
305A LEU* 3.3 13.7 + - - +
316A ALA* 4.1 8.8 - - - +
319A ALA* 4.0 24.7 - - + -
320A VAL* 4.1 15.9 - - + +
323A ILE* 4.1 20.4 - - + -
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Residues in contact with VAL 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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298A CYS 2.7 22.2 + - - +
299A ARG 4.0 2.5 - - - +
301A LEU* 1.3 72.3 - - - +
303A GLU* 1.3 66.3 + - + +
305A LEU* 3.1 27.3 + - + +
320A VAL* 4.4 5.4 - - + -
334A ILE* 4.0 19.5 - - + +
337A CYS* 3.6 33.7 - - + +
338A SER 4.2 2.2 - - - +
339A ALA* 3.4 42.0 - - + -
342A SER* 4.2 9.9 + - - +
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Residues in contact with GLU 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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264A PHE* 5.8 0.2 - - - -
299A ARG* 2.9 48.2 + - + +
300A ARG* 2.8 38.8 + - - +
302A VAL* 1.3 79.2 - - + +
304A LEU* 1.3 62.8 + - - +
306A MET* 3.2 23.2 + - - +
307A HIS 4.2 1.0 + - - -
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Residues in contact with LEU 304 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
263A LEU* 3.8 33.2 - - + +
271A LEU* 4.1 18.2 - - + -
275A CYS* 4.1 11.7 - - - -
300A ARG* 2.8 46.0 + - - +
301A LEU* 3.2 7.8 + - - +
303A GLU* 1.3 73.1 - - - +
305A LEU* 1.4 59.4 + - - +
306A MET 3.0 5.2 - - - -
307A HIS* 3.0 36.5 + - + +
312A VAL* 4.0 18.3 - - + +
313A VAL* 3.9 10.0 - - - +
316A ALA* 4.1 12.6 - - + -
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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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301A LEU 3.3 7.8 + - - +
302A VAL* 3.1 27.9 + - + +
304A LEU* 1.4 75.9 - - - +
306A MET* 1.3 59.6 + - - +
307A HIS 3.4 1.1 - - - +
313A VAL* 3.9 12.7 - - - +
316A ALA* 3.9 8.1 - - + +
317A LEU* 3.6 44.4 - - + +
320A VAL* 4.1 14.6 - - + -
339A ALA* 4.8 1.8 - - + -
342A SER* 4.1 22.9 - - - -
343A LEU* 4.2 23.3 - - + -
345A HIS* 5.0 0.3 - - - -
346A LEU* 3.7 32.6 - - + +
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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