Contacts of the helix formed by residues 318 - 327 (chain A) in PDB entry 1IVS
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 ARG 318 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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196A LYS* 5.1 2.2 + - - +
198A TYR* 5.2 11.6 - - - -
215A VAL* 2.6 38.1 + - - +
216A ARG* 3.1 26.5 - - - +
217A PRO* 3.9 13.9 - - + -
218A GLU* 3.1 30.1 + - + +
315A PHE* 2.8 41.3 + - + +
317A ALA* 1.3 79.2 - - - +
319A ARG* 1.3 75.5 + - + +
321A ALA* 3.5 4.3 - - - -
322A VAL* 2.9 28.1 + - + +
339A ILE* 5.9 1.2 - - - +
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Residues in contact with ARG 319 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
313A ASP* 4.7 0.6 + - - -
315A PHE* 3.2 18.7 + - - +
316A GLU* 2.6 69.4 + - - +
317A ALA 3.4 0.2 - - - -
318A ARG* 1.3 86.6 - - + +
320A LYS* 1.3 64.8 + - + +
321A ALA 3.0 0.3 + - - -
322A VAL* 3.0 12.4 + - - +
323A GLU* 3.4 16.2 + - - +
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Residues in contact with LYS 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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308A ALA 5.6 7.2 + - - +
309A LEU* 4.5 14.6 - - + +
312A LEU* 5.6 9.7 - - + +
316A GLU* 4.4 18.1 + - + +
317A ALA 4.1 2.0 + - - -
318A ARG 3.5 0.2 - - - -
319A ARG* 1.3 80.7 - - + +
321A ALA* 1.3 59.5 + - - +
322A VAL 3.4 0.2 - - - -
323A GLU* 4.1 9.2 - - + -
324A LEU* 2.8 38.3 + - + +
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Residues in contact with ALA 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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217A PRO* 4.5 5.6 - - + -
218A GLU* 4.6 8.3 - - + +
221A PHE* 5.1 0.2 - - + -
309A LEU* 4.3 20.6 - - + -
317A ALA 2.8 23.7 + - - +
318A ARG* 3.3 12.1 - - - +
319A ARG 3.0 0.8 - - - -
320A LYS* 1.3 77.3 - - - +
322A VAL* 1.3 64.0 + - - +
324A LEU* 3.4 10.9 + - - +
325A PHE* 2.9 36.2 + - + -
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Residues in contact with VAL 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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198A TYR* 3.2 37.9 - - + +
217A PRO* 4.0 13.9 - - + -
318A ARG* 2.9 21.0 + - + +
319A ARG* 3.6 4.9 - - - +
321A ALA* 1.3 71.9 - - - +
323A GLU* 1.3 70.8 + - - +
324A LEU 3.0 1.6 - - - -
325A PHE* 2.6 33.3 + - + +
326A ARG* 3.0 18.6 + - - +
331A LEU* 3.5 28.7 - - + -
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Residues in contact with GLU 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 ARG 3.7 14.0 - - - +
320A LYS* 4.1 9.6 - - + +
322A VAL* 1.3 95.1 - - - +
324A LEU* 1.3 65.6 + - + +
325A PHE 3.3 0.5 + - - -
326A ARG* 3.7 31.4 + - - -
327A GLU* 2.9 40.4 + - - +
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Residues in contact with LEU 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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247A LEU* 3.8 29.3 - - + +
309A LEU* 5.9 8.7 - - + -
320A LYS* 2.8 32.5 - - + +
321A ALA* 3.4 9.5 + - - +
322A VAL 3.0 1.0 - - - -
323A GLU* 1.3 83.0 - - + +
325A PHE* 1.3 57.8 + - - +
327A GLU* 5.1 5.2 - - - +
328A ALA* 2.9 23.4 - - - +
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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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200A LEU* 3.6 32.1 - - + -
217A PRO* 3.9 25.4 - - + -
220A VAL* 3.7 26.2 - - + -
221A PHE* 4.2 11.0 - + - -
246A PRO* 3.4 23.6 - - + -
247A LEU* 3.2 33.0 - - + -
321A ALA* 2.9 29.6 - - + -
322A VAL* 2.6 20.7 + - + +
324A LEU* 1.3 71.3 - - - +
326A ARG* 1.3 54.3 + - - +
328A ALA* 3.0 5.0 + - - +
329A GLY 2.6 29.1 + - - -
330A HIS* 2.8 15.3 + + + -
331A LEU* 4.0 3.6 - - + -
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Residues in contact with ARG 326 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
322A VAL* 3.0 12.4 + - - +
323A GLU* 3.7 35.6 + - - +
325A PHE* 1.3 74.2 - - - +
327A GLU* 1.3 73.3 + - + +
328A ALA 2.8 4.0 - - - -
329A GLY* 2.5 25.7 + - - -
331A LEU* 3.4 42.9 - - + +
334A GLU* 3.0 27.1 + - - -
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Residues in contact with GLU 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 GLU* 2.9 26.3 + - - +
324A LEU* 5.0 6.1 - - - +
326A ARG* 1.3 84.7 - - + +
328A ALA* 1.3 56.4 + - - +
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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