Contacts of the strand formed by residues 251 - 258 (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 ALA 251 (chain N).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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250N LEU* 1.3 73.8 - - - +
252N HIS* 1.3 62.0 + - - +
253N VAL* 4.2 2.6 - - + +
324N PHE* 3.8 0.7 - - - +
325N VAL* 3.3 7.4 - - - +
326N CYS* 2.9 37.2 + - - +
327N ASP 5.2 0.9 - - - +
331N ILE* 3.8 21.8 - - + -
425N PHE 3.5 4.9 - - - -
427N PRO* 3.8 13.1 - - + +
428N ILE* 3.7 25.4 - - + -
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Residues in contact with HIS 252 (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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145N MET* 3.3 38.1 - - + +
146N ARG* 3.6 27.0 + - + -
149N VAL* 3.8 16.6 - - + +
250N LEU* 4.3 3.0 - - + +
251N ALA* 1.3 78.4 - - - +
253N VAL* 1.3 66.8 + - - +
323N HIS* 3.0 24.3 + + - +
324N PHE 3.5 3.1 - - - -
325N VAL* 3.4 31.3 - - + +
424N GLY* 3.5 1.6 - - - -
425N PHE* 3.0 36.6 + - + +
428N ILE* 4.7 0.2 - - - +
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Residues in contact with VAL 253 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149N VAL* 4.5 0.2 - - - -
251N ALA* 5.0 3.6 - - + -
252N HIS* 1.3 83.2 - - - +
254N ALA* 1.3 70.1 + - - +
255N ILE* 4.3 0.9 - - + +
322N ALA 4.1 0.3 - - - +
323N HIS* 3.2 6.2 - - - -
324N PHE* 2.9 60.5 + - + -
331N ILE* 4.1 15.3 - - + -
335N MET* 3.9 27.8 - - + -
422N VAL* 4.5 4.0 - - + -
423N ALA 3.2 10.3 - - - +
424N GLY* 4.6 4.7 - - - -
428N ILE* 4.8 8.1 - - + -
431N LEU* 4.1 13.7 - - + -
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Residues in contact with ALA 254 (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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149N VAL* 4.2 29.1 - - + +
150N PHE* 4.7 6.3 - - + -
153N LEU* 3.8 24.1 - - + +
253N VAL* 1.3 77.1 - - - +
255N ILE* 1.3 61.1 + - - +
322N ALA 3.5 7.6 - - - +
323N HIS* 4.2 7.4 - - + +
422N VAL* 3.5 2.6 - - - +
423N ALA* 2.8 33.6 + - + +
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Residues in contact with ILE 255 (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* 4.8 0.2 - - - -
253N VAL* 5.1 2.2 - - + -
254N ALA* 1.3 75.6 - - - +
256N ALA* 1.3 66.4 + - - +
310N PHE* 3.8 1.5 - - - -
321N GLY* 3.2 2.4 - - - -
322N ALA 3.0 36.8 + - - +
324N PHE* 5.2 2.0 - - + -
335N MET* 4.0 26.2 - - + -
338N LEU* 3.8 25.6 - - + -
339N GLN* 4.5 3.4 - - - +
342N TRP* 3.8 21.1 - - + -
420N PRO* 3.9 17.3 - - + -
421N ALA 3.4 10.5 - - - +
422N VAL* 4.1 8.7 - - + -
437N ILE* 3.9 27.8 - - + -
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Residues in contact with ALA 256 (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* 4.2 8.5 - - + -
236N PHE* 3.7 3.4 - - - -
255N ILE* 1.3 78.8 - - - +
257N VAL* 1.3 70.2 + - - +
310N PHE* 3.9 14.4 - - + -
319N LEU* 3.9 13.9 - - + -
320N LEU 3.2 24.2 - - - +
321N GLY* 4.0 0.4 - - - -
342N TRP* 5.3 1.8 - - - -
420N PRO* 3.2 3.4 - - - +
421N ALA* 2.7 38.7 + - + +
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Residues in contact with VAL 257 (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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236N PHE* 3.8 7.9 - - - -
256N ALA* 1.3 79.7 - - - +
258N GLU* 1.3 64.2 + - - +
259N GLY 3.4 0.3 + - - -
319N LEU* 3.7 4.3 - - - -
320N LEU* 2.8 49.3 + - + +
342N TRP* 5.6 1.3 - - + -
414N TYR 3.3 28.7 - - - +
415N PHE* 3.9 17.7 - - + -
418N GLN* 4.4 9.0 - - + -
419N CYS 4.5 3.6 - - - +
420N PRO* 4.2 9.0 - - + -
441N MET* 3.4 33.4 - - + -
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Residues in contact with GLU 258 (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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234N CYS 4.6 4.3 - - - +
236N PHE* 3.4 48.7 + - + +
257N VAL* 1.3 80.7 - - - +
259N GLY* 1.3 63.8 + - - +
316N ASP 4.5 2.9 - - - +
317N THR* 2.8 34.8 + - - +
318N GLY 3.5 3.8 - - - +
414N TYR* 3.7 11.8 + - - +
419N CYS 5.1 0.4 + - - -
24R SER* 4.3 12.6 + - - -
25R SER* 5.1 2.0 + - - -
26R LYS* 3.3 52.0 + - - +
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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