Contacts of the strand formed by residues 351 - 357 (chain A) in PDB entry 4PE5
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 TYR 351 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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124A ARG* 4.1 10.8 + - - -
142A PRO* 3.1 26.3 - - + +
143A PRO 4.5 0.5 + - - -
146A HIS* 4.0 14.4 + - - +
147A GLN* 3.9 21.1 + - + -
150A VAL* 3.4 32.8 - - + -
269A LEU* 4.1 19.1 - - + -
270A GLN 3.6 8.7 - - - +
271A LEU* 3.5 30.5 - - + -
272A ILE* 4.0 4.7 - - - -
349A ALA* 3.8 16.0 + - + +
350A GLN* 1.3 83.5 - - - +
352A SER* 1.3 65.1 + - - +
366A ILE* 3.3 5.9 - - - +
367A TYR* 2.9 45.2 + + + +
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Residues in contact with SER 352 (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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269A LEU* 3.3 6.2 - - - +
270A GLN* 2.9 44.5 + - - -
272A ILE* 3.6 19.6 - - - +
351A TYR* 1.3 72.2 - - - +
353A ILE* 1.3 60.9 + - - +
354A MET* 3.7 23.6 + - - +
363A GLN* 3.6 20.3 + - - -
365A GLY 3.8 4.7 - - - -
366A ILE* 4.7 1.9 - - - +
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Residues in contact with ILE 353 (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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150A VAL* 4.5 13.2 - - + -
267A ILE* 3.7 26.9 - - + -
268A GLY 3.6 4.9 - - - +
269A LEU* 3.8 16.2 - - + -
351A TYR 4.3 0.2 - - - +
352A SER* 1.3 70.5 - - - +
354A MET* 1.3 57.3 + - - +
363A GLN* 3.6 2.3 - - - -
364A VAL* 2.8 42.8 + - + +
365A GLY* 2.8 25.8 + - - +
366A ILE 4.0 14.8 - - - +
367A TYR* 4.1 9.6 - - + +
372A VAL* 3.9 28.7 - - + -
379A ILE* 6.1 0.7 - - + -
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Residues in contact with MET 354 (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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254A ILE* 4.6 4.9 - - + +
266A ILE 3.8 0.7 - - - +
267A ILE* 3.5 5.4 - - - +
268A GLY 2.9 37.9 + - - +
270A GLN* 3.7 39.0 - - + +
352A SER* 3.7 24.0 - - - +
353A ILE* 1.3 73.6 - - - +
355A ASN* 1.3 60.4 + - - +
361A LEU* 4.4 29.3 - - + +
362A VAL 3.4 4.3 - - - -
363A GLN* 3.6 44.9 - - + +
364A VAL* 4.4 2.2 - - - -
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Residues in contact with ASN 355 (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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265A GLY* 3.3 15.2 - - - +
266A ILE 2.8 23.6 - - - +
267A ILE* 3.9 11.7 - - + -
353A ILE 4.4 0.2 + - - -
354A MET* 1.3 73.9 - - - +
356A LEU* 1.3 63.4 + - - +
357A GLN* 3.2 19.3 + - - +
361A LEU* 4.1 2.7 - - - -
362A VAL* 2.5 42.8 + - - +
364A VAL* 3.4 21.1 - - + -
379A ILE* 3.7 5.9 - - - +
380A ILE 2.9 40.6 + - - +
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Residues in contact with LEU 356 (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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259A LEU* 4.6 15.0 - - + +
262A ALA* 3.6 25.8 - - + +
263A PRO 3.3 24.5 - - - +
264A ASP* 3.7 6.4 - - + +
265A GLY* 2.8 30.0 + - - +
266A ILE* 3.3 21.7 + - + +
355A ASN* 1.3 73.6 + - - +
357A GLN* 1.3 59.6 + - - +
359A ARG* 3.6 27.8 - - - +
360A LYS 3.3 23.6 - - - +
361A LEU* 3.9 20.4 - - + +
380A ILE* 5.7 0.5 - - - +
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Residues in contact with GLN 357 (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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264A ASP* 5.5 0.2 - - - -
355A ASN* 3.2 29.9 - - - +
356A LEU* 1.3 76.3 - - - +
358A ASN* 1.3 75.7 + - - +
359A ARG 3.2 0.4 - - - -
360A LYS* 2.7 30.0 + - - +
362A VAL* 3.7 29.2 - - + +
364A VAL* 3.9 3.8 - - - +
377A ARG* 3.3 24.2 + - - +
378A LYS 3.1 24.9 + - - +
380A ILE* 3.4 33.8 - - + +
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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