Contacts of the helix formed by residues 320 - 329 (chain A) in PDB entry 5PLL
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 SER 320 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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161A GLN* 2.8 31.2 + - - -
173A GLU 5.1 1.5 - - - +
174A GLY* 4.7 9.6 - - - -
175A VAL* 3.0 21.1 + - - -
318A THR* 3.4 21.0 + - - -
319A PHE* 1.3 76.7 - - - +
321A MET* 1.3 58.8 + - - +
322A ASP 3.5 0.5 + - - -
323A ALA* 3.8 9.6 + - - +
324A PHE* 3.7 24.1 - - - -
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Residues in contact with MET 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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195A ASP* 3.7 34.8 - - + +
196A MET* 4.3 10.5 - - + +
309A GLN* 3.4 28.5 - - - +
317A VAL* 3.6 23.1 - - + -
318A THR* 3.2 18.8 + - + +
319A PHE 3.1 1.6 - - - -
320A SER* 1.3 75.2 - - - +
322A ASP* 1.3 63.8 + - - +
324A PHE* 3.0 31.8 + - + +
325A VAL* 3.1 25.3 + - + +
336A TRP* 3.6 29.6 - - + +
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Residues in contact with ASP 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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173A GLU* 4.6 0.4 - - - +
319A PHE* 3.1 47.9 + - + +
321A MET* 1.3 76.9 - - - +
323A ALA* 1.3 56.8 + - - +
325A VAL* 3.3 0.9 + - - +
326A ARG* 2.9 46.8 + - - +
333A TYR* 2.6 40.3 + - - -
336A TRP* 3.6 22.4 - - + -
337A LYS* 3.8 10.0 - - - +
340A GLN* 5.8 1.0 - - - +
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Residues in contact with ALA 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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164A LEU* 5.8 0.2 - - - +
172A ILE* 3.8 36.9 - - + +
173A GLU* 3.7 16.3 + - - +
319A PHE 4.4 0.6 + - - -
320A SER 3.8 5.6 + - - +
321A MET 3.3 0.6 - - - -
322A ASP* 1.3 78.7 - - - +
324A PHE* 1.4 64.4 + - - +
326A ARG* 3.3 22.9 - - - +
327A ILE* 3.0 29.1 + - - +
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Residues in contact with PHE 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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160A ILE* 3.5 33.4 - - + -
161A GLN* 3.8 18.6 - - + -
164A LEU* 3.7 18.4 - - + -
172A ILE* 3.9 19.5 - - + -
173A GLU 5.8 0.2 - - - -
196A MET* 3.7 30.5 - - + +
198A LEU* 4.2 19.3 - - + -
300A TRP* 4.8 6.5 - + + -
318A THR* 6.2 0.9 - - + -
320A SER* 3.7 26.7 - - - -
321A MET* 3.0 24.0 + - + +
323A ALA* 1.4 75.5 - - - +
325A VAL* 1.3 56.4 + - - +
327A ILE* 5.3 0.2 - - - -
328A LEU* 2.9 39.3 + - + +
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Residues in contact with VAL 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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196A MET* 3.9 17.3 - - + -
309A GLN* 4.1 5.8 - - + +
321A MET* 3.1 38.3 + - + +
322A ASP 3.9 4.7 - - - +
324A PHE* 1.3 72.9 - - - +
326A ARG* 1.4 62.8 + - - +
329A GLN* 2.8 51.0 + - + +
332A ARG* 4.6 2.5 - - + -
333A TYR* 3.9 26.9 - - + +
336A TRP* 3.9 29.4 - - + -
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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
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172A ILE* 4.3 10.1 - - - +
173A GLU* 2.8 42.4 + - - -
319A PHE* 5.4 0.4 - - - -
322A ASP* 2.9 42.6 + - - +
323A ALA* 3.3 22.3 - - - +
325A VAL* 1.4 79.4 - - - +
327A ILE* 1.3 71.7 + - + +
330A PRO* 3.8 20.1 - - - +
333A TYR* 3.6 42.1 - - + -
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Residues in contact with ILE 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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164A LEU* 5.3 6.7 - - + -
168A CYS* 5.6 3.8 - - + -
170A VAL* 4.0 35.9 - - + -
172A ILE* 4.0 22.0 - - + -
323A ALA 3.0 19.0 + - - +
324A PHE* 4.5 0.7 - - - +
326A ARG* 1.3 96.6 - - + +
328A LEU* 1.3 73.7 + - + +
330A PRO* 3.5 10.0 - - - +
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Residues in contact with LEU 328 (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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164A LEU* 4.0 22.9 - - + -
168A CYS* 4.9 5.4 - - - -
196A MET* 4.3 2.7 - - + -
300A TRP* 3.6 33.9 - - + -
301A ILE* 4.4 13.5 - - + +
304A GLY* 3.9 20.2 - - - +
305A LYS* 4.1 39.4 - - + +
324A PHE* 2.9 20.5 + - - +
327A ILE* 1.3 86.0 - - + +
329A GLN* 1.3 67.2 + - + +
330A PRO* 3.4 5.3 - - - +
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Residues in contact with GLN 329 (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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196A MET* 3.1 21.6 - - + +
304A GLY 3.3 9.9 + - - +
305A LYS 3.3 22.5 + - - +
307A ALA 2.8 26.6 + - - +
309A GLN* 2.7 32.1 + - - +
325A VAL* 2.8 25.1 + - + +
328A LEU* 1.3 80.1 - - - +
330A PRO* 1.4 64.5 - - - +
331A GLU 3.2 2.5 - - - -
332A ARG* 2.9 35.3 + - + +
333A TYR 3.2 8.1 + - - -
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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