Contacts of the helix formed by residues 297 - 308 (chain A) in PDB entry 4AF3
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 PRO 297 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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174A GLU* 3.5 44.6 - - + +
267A LEU* 4.6 9.9 - - + -
295A SER 3.8 8.1 - - - +
296A VAL* 1.3 86.4 - - + +
298A THR* 1.3 68.1 + - - +
299A GLY 4.6 1.6 - - - +
300A ALA* 2.8 22.8 + - + +
301A GLN 3.2 8.4 + - - -
326A TRP* 4.0 13.2 - - + +
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Residues in contact with THR 298 (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 VAL 3.6 2.0 + - - -
297A PRO* 1.3 70.1 - - - +
299A GLY* 1.3 66.5 + - - +
301A GLN* 3.0 27.5 + - - +
302A ASP* 3.0 15.1 + - + +
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Residues in contact with GLY 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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297A PRO* 3.0 2.2 + - - +
298A THR* 1.3 80.8 - - - +
300A ALA* 1.3 60.4 + - - +
302A ASP* 3.5 5.0 + - - +
303A LEU* 3.3 6.9 + - - +
324A HIS* 3.1 25.6 - - - -
326A TRP* 3.6 29.5 - - - +
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Residues in contact with ALA 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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263A CYS* 4.9 0.7 - - - -
267A LEU* 3.4 32.8 - - + -
296A VAL* 3.7 7.2 - - + -
297A PRO* 2.8 17.6 + - + +
299A GLY* 1.3 69.0 - - - -
301A GLN* 1.3 65.5 + - - +
303A LEU* 3.2 3.5 + - - +
304A ILE* 2.8 33.8 + - + +
326A TRP* 3.7 27.8 - - + -
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Residues in contact with GLN 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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292A PHE* 3.5 47.8 + - + +
293A PRO 4.7 3.8 + - - -
296A VAL* 3.2 36.7 + - + +
297A PRO 3.2 4.2 + - - +
298A THR* 3.0 19.6 + - - +
300A ALA* 1.3 74.7 - - - +
302A ASP* 1.3 54.6 + - - +
305A SER* 2.8 38.9 + - - -
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Residues in contact with ASP 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 THR* 3.0 13.8 + - + +
299A GLY* 3.5 12.8 - - - +
300A ALA 3.1 0.2 - - - -
301A GLN* 1.3 75.6 - - - +
303A LEU* 1.3 64.5 + - - +
305A SER* 3.9 3.9 - - - -
306A LYS* 2.8 63.8 + - - +
324A HIS* 2.7 26.2 + - + +
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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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181A MET* 4.3 12.3 - - + -
263A CYS* 4.1 24.7 - - - -
299A GLY 3.3 9.2 + - - +
300A ALA* 3.2 7.6 + - - +
302A ASP* 1.3 75.2 - - - +
304A ILE* 1.3 67.4 + - - +
306A LYS* 3.0 15.1 + - - +
307A LEU* 3.0 25.6 + - + +
316A LEU* 3.7 26.5 - - + -
321A VAL* 4.0 18.8 - - + -
324A HIS* 3.6 25.7 + - + +
326A TRP* 4.3 4.5 - - + -
327A VAL* 3.7 24.2 - - + -
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Residues in contact with ILE 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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260A GLY* 4.0 8.7 - - - +
263A CYS* 3.7 28.7 - - + +
264A TYR* 3.3 37.9 - - + +
267A LEU* 4.7 2.7 - - + -
290A LEU* 4.1 2.9 - - + -
292A PHE* 3.7 28.7 - - + -
296A VAL* 4.9 2.7 - - + -
300A ALA* 2.8 30.6 + - + +
303A LEU* 1.3 72.7 - - + +
305A SER* 1.3 58.5 + - - +
307A LEU* 3.1 5.8 + - - +
308A LEU* 2.9 51.7 + - + +
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Residues in contact with SER 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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290A LEU* 4.0 11.6 - - - +
292A PHE* 3.5 17.9 - - - -
301A GLN 2.8 23.8 + - - -
302A ASP* 3.9 5.4 - - - -
304A ILE* 1.3 74.4 - - - +
306A LYS* 1.3 58.7 + - - +
308A LEU* 4.1 3.6 - - - +
309A ARG* 3.1 29.6 + - - -
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Residues in contact with LYS 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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302A ASP* 2.8 54.0 + - - +
303A LEU* 3.0 8.3 + - - +
305A SER* 1.3 76.7 - - - +
307A LEU* 1.3 62.5 + - - +
309A ARG* 3.4 21.4 - - - +
314A GLU 3.8 2.6 - - - +
315A ARG* 3.7 0.3 - - - -
316A LEU* 3.2 50.2 + - + -
324A HIS* 4.8 4.8 + - + +
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Residues in contact with LEU 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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181A MET* 5.5 0.2 - - - -
256A LEU* 3.4 25.8 - - + +
257A TRP* 4.4 0.9 - - - -
259A ILE* 3.5 17.9 - - + +
260A GLY* 3.3 32.1 - - - +
263A CYS* 5.6 0.4 - - + -
303A LEU* 3.0 36.0 + - + +
304A ILE* 3.1 5.8 + - - +
306A LYS* 1.3 77.9 - - - +
308A LEU* 1.3 61.3 + - - +
309A ARG 2.9 8.9 + - - -
315A ARG* 3.1 25.1 - - - +
316A LEU* 3.5 33.0 - - + +
321A VAL* 3.8 11.9 - - + -
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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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257A TRP* 3.2 55.2 - - + +
260A GLY* 3.7 16.6 - - - -
261A VAL* 3.8 4.7 - - + +
272A PRO* 4.3 9.6 - - + -
273A PHE* 4.1 17.9 - - + -
288A VAL* 3.3 21.9 - - + +
290A LEU* 3.9 31.7 - - + +
304A ILE* 2.9 28.5 + - + +
305A SER* 4.1 3.5 - - - +
306A LYS 3.7 0.4 - - - -
307A LEU* 1.3 71.2 - - - +
309A ARG* 1.3 67.3 + - - +
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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