Contacts of the helix formed by residues 317 - 327 (chain A) in PDB entry 4BM9
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 GLN 317 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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313A ASN* 3.3 15.2 + - - +
314A ARG* 2.8 18.5 + - - +
316A GLN* 1.3 80.2 - - + +
318A TYR* 1.3 63.1 + - - +
319A GLY 3.4 2.0 - - - -
320A ALA* 3.2 11.7 + - + +
321A GLU* 2.9 24.8 + - + +
331A LEU* 3.8 27.3 - - + +
332A CYS 4.8 4.7 + - - +
333A PRO* 5.7 1.0 - - - +
335A PRO* 4.9 10.7 + - - +
338A GLY* 4.7 15.9 - - - -
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Residues in contact with TYR 318 (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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272A LEU* 3.8 22.0 - - + -
275A ARG* 3.1 70.9 + - - +
277A PHE* 3.3 33.6 + + + -
285A TYR* 3.3 50.3 - + + -
314A ARG 3.4 3.3 + - - -
315A TYR* 3.1 19.3 + + - +
316A GLN 3.3 2.2 + - - -
317A GLN* 1.3 78.5 - - - +
319A GLY* 1.3 57.1 + - - +
321A GLU* 3.4 0.4 + - - -
322A GLU* 2.9 43.1 + - - +
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Residues in contact with GLY 319 (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 TYR* 3.7 30.7 + - - -
316A GLN 5.3 0.2 + - - -
317A GLN 3.4 0.4 - - - -
318A TYR* 1.3 78.8 - - - +
320A ALA* 1.3 61.5 + - - +
322A GLU* 3.4 3.4 + - - +
323A CYS* 3.3 19.6 + - - +
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Residues in contact with ALA 320 (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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317A GLN* 3.2 14.8 + - + +
319A GLY* 1.3 76.6 - - - +
321A GLU* 1.3 64.0 + - - +
323A CYS* 3.0 17.5 + - - +
324A VAL* 3.1 17.5 + - + +
331A LEU* 4.9 7.9 - - + -
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Residues in contact with GLU 321 (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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275A ARG* 3.6 16.2 + - - +
314A ARG* 2.9 53.5 + - - +
317A GLN* 2.9 19.3 + - + +
320A ALA* 1.3 78.0 - - - +
322A GLU* 1.3 58.1 + - - +
324A VAL* 3.2 4.2 + - + +
325A LEU* 2.9 46.8 + - + +
331A LEU* 3.9 30.5 + - + +
369A LYS* 3.2 21.4 + - - +
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Residues in contact with GLU 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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275A ARG* 2.9 45.4 + - - +
285A TYR* 4.9 7.2 - - + +
318A TYR* 2.9 42.5 + - + +
319A GLY* 3.7 8.1 - - - +
320A ALA 3.2 0.2 - - - -
321A GLU* 1.3 76.1 - - - +
323A CYS* 1.3 60.9 + - - +
325A LEU* 3.6 7.4 + - - +
326A GLN* 3.2 27.5 + - - +
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Residues in contact with CYS 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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319A GLY 3.3 8.9 + - - +
320A ALA* 3.0 12.7 + - - +
322A GLU* 1.3 76.1 - - - +
324A VAL* 1.3 66.6 - - + +
326A GLN* 3.1 43.1 + - - +
327A MET* 3.4 19.5 - - - -
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Residues in contact with VAL 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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320A ALA* 3.1 14.1 + - + +
321A GLU* 3.6 11.2 - - - +
323A CYS* 1.3 76.7 + - + +
325A LEU* 1.3 54.5 + - + +
327A MET* 3.1 23.5 - - + +
329A GLY* 2.8 53.5 + - - +
330A VAL 3.4 22.2 - - - +
331A LEU* 3.9 14.6 - - + +
340A GLY* 5.3 6.7 - - - -
341A LEU 5.0 2.0 - - - +
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Residues in contact with LEU 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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275A ARG* 3.7 35.2 - - + +
314A ARG* 5.3 0.4 - - - +
321A GLU* 2.9 42.4 + - + +
322A GLU* 3.8 10.8 - - - +
323A CYS 3.2 0.2 - - - +
324A VAL* 1.3 74.7 - - + +
326A GLN* 1.3 56.5 - - - +
327A MET 3.1 5.2 - - - -
328A GLY* 2.9 19.6 + - - -
329A GLY 3.6 15.9 - - - +
330A VAL* 5.2 8.1 - - + -
366A ARG* 6.0 2.7 - - + +
369A LYS* 6.3 2.5 - - + -
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Residues in contact with GLN 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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322A GLU* 3.2 15.6 + - - +
323A CYS* 3.1 44.0 + - - +
325A LEU* 1.3 76.0 - - - +
327A MET* 1.3 59.2 + - + +
328A GLY 3.2 1.3 + - - -
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Residues in contact with MET 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 CYS* 3.4 25.3 - - - -
324A VAL* 3.1 28.4 + - + +
325A LEU 3.1 0.8 - - - -
326A GLN* 1.3 78.9 - - + +
328A GLY* 1.3 57.7 + - - +
329A GLY* 3.6 8.5 - - - +
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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