Contacts of the strand formed by residues 318 - 326 (chain N) in PDB entry 1PP9
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 GLY 318 (chain N).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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158N PHE* 4.1 2.3 - - - -
258N GLU* 3.5 9.4 - - - +
259N GLY* 2.6 33.9 + - - -
261N GLY 5.1 0.2 - - - -
312N ILE 3.0 14.4 - - - -
313N CYS* 4.4 0.4 - - - -
314N TYR* 4.1 11.2 - - - -
317N THR* 1.3 82.6 + - - +
319N LEU* 1.3 65.6 + - - +
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Residues in contact with LEU 319 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153N LEU* 3.8 22.2 - - + -
154N HIS* 3.6 43.1 - - + +
157N ALA* 3.8 18.6 - - + -
158N PHE* 3.6 24.9 - - + -
236N PHE* 4.0 11.4 - - + -
256N ALA* 3.9 15.3 - - + -
257N VAL 3.7 1.3 - - - -
310N PHE* 3.4 13.7 - - + -
311N ASN* 4.6 1.3 - - - -
312N ILE* 2.7 45.3 + - + +
314N TYR* 5.0 0.9 - - + -
318N GLY* 1.3 78.0 - - - +
320N LEU* 1.3 60.4 + - - +
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Residues in contact with LEU 320 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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256N ALA* 3.2 1.9 - - - +
257N VAL* 2.8 45.0 + - + +
259N GLY* 4.3 8.1 - - - -
270N LEU* 3.7 39.3 - - + -
274N ASN* 3.6 32.1 - - - +
310N PHE 3.6 2.2 - - - +
311N ASN* 3.6 23.1 - - - +
318N GLY 4.1 0.8 + - - -
319N LEU* 1.3 72.0 - - - +
321N GLY* 1.3 58.8 + - - +
414N TYR* 3.9 18.2 - - + -
415N PHE* 3.6 26.6 - - + -
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Residues in contact with GLY 321 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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255N ILE 3.2 12.3 - - - -
274N ASN* 4.5 2.3 + - - +
309N THR* 3.2 8.5 - - - +
310N PHE* 2.7 46.3 + - - +
320N LEU* 1.3 78.0 - - - +
322N ALA* 1.3 57.7 + - - +
342N TRP* 3.9 16.8 + - - -
415N PHE* 4.8 2.2 - - - -
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Residues in contact with ALA 322 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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253N VAL 4.1 0.2 - - - +
254N ALA* 3.5 0.7 - - - -
255N ILE* 3.0 35.6 + - - +
307N PHE* 5.6 3.8 - - + -
308N GLN 3.1 14.8 - - - +
309N THR* 3.9 9.0 - - + -
310N PHE* 3.3 11.5 - - - -
321N GLY* 1.3 75.3 - - - +
323N HIS* 1.3 61.0 + - - +
324N PHE* 5.4 1.5 - - + -
338N LEU* 3.9 35.9 - - + -
342N TRP* 4.1 2.3 - - + -
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Residues in contact with HIS 323 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146N ARG* 3.9 17.7 - - + +
149N VAL* 3.6 24.0 - - + +
150N PHE* 3.6 27.8 - + + -
252N HIS* 3.0 26.9 + + - -
253N VAL 3.2 20.4 - - - -
254N ALA* 4.4 2.0 - - + -
306N SER* 5.4 0.6 + - - -
307N PHE* 3.0 5.6 - - - +
308N GLN* 2.8 52.4 + - + +
310N PHE* 3.8 0.4 - - + -
322N ALA* 1.3 76.6 - - - +
324N PHE* 1.3 65.3 + - - +
325N VAL* 3.5 26.4 - - + +
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Residues in contact with PHE 324 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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252N HIS* 3.5 3.5 - - - -
253N VAL* 2.9 70.7 + - + -
255N ILE* 5.2 1.3 - - + -
304N CYS* 4.9 0.7 - - + -
306N SER 3.2 12.1 - - - +
307N PHE* 3.6 11.7 - - + +
322N ALA* 5.4 1.8 - - + -
323N HIS* 1.3 82.2 + - - +
325N VAL* 1.3 65.3 + - - +
326N CYS* 3.8 24.2 - - + -
331N ILE* 4.1 13.0 - - + -
334N MET* 3.7 43.7 - - + -
335N MET* 4.2 20.0 - - + -
338N LEU* 4.4 20.0 - - + -
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Residues in contact with VAL 325 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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250N LEU* 4.0 25.8 - - + -
251N ALA 3.3 7.4 - - - +
252N HIS* 3.4 40.2 - - + +
304N CYS* 3.3 3.5 - - - +
305N GLN* 2.8 32.0 + - + -
306N SER* 2.8 27.9 + - - +
323N HIS* 3.5 13.5 - - + -
324N PHE* 1.3 78.5 - - - +
326N CYS* 1.3 65.6 + - - +
41V PRO* 4.6 6.3 - - + -
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Residues in contact with CYS 326 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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250N LEU* 3.7 10.8 - - - -
251N ALA* 2.9 36.6 + - - +
303N LEU 3.3 23.3 - - - +
304N CYS* 3.8 7.4 - - + +
305N GLN* 4.4 2.2 - - - +
324N PHE* 3.8 20.6 - - + -
325N VAL* 1.3 76.9 - - - +
327N ASP* 1.3 76.1 + - - +
330N SER* 3.9 2.7 - - - -
331N ILE* 3.7 31.0 - - - -
334N MET* 4.5 0.7 - - + -
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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