Contacts of the strand formed by residues 351 - 357 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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124C ARG* 4.4 5.5 + - - -
142C PRO* 3.1 28.3 - - + +
143C PRO 4.5 0.7 + - - -
146C HIS* 4.0 15.0 - - - +
147C GLN* 3.9 24.0 + - + -
150C VAL* 3.4 31.6 - - + -
269C LEU* 4.2 19.1 - - + -
270C GLN 3.6 7.9 - - - +
271C LEU* 3.4 32.5 - - + -
272C ILE* 4.0 4.0 - - - -
349C ALA* 3.8 13.0 - - + +
350C GLN* 1.3 83.8 - - - +
352C SER* 1.3 65.7 + - - +
353C ILE 3.6 0.2 + - - -
366C ILE* 3.3 5.5 - - - +
367C TYR* 2.9 41.2 + - + -
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Residues in contact with SER 352 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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269C LEU* 3.3 6.9 - - - +
270C GLN* 2.9 43.8 + - - -
272C ILE* 3.6 20.3 - - - +
351C TYR* 1.3 72.6 - - - +
353C ILE* 1.3 61.1 + - - +
354C MET* 3.6 23.2 + - - +
363C GLN* 3.6 19.9 + - - -
365C GLY 3.8 4.3 - - - -
366C ILE* 4.6 1.6 - - - +
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Residues in contact with ILE 353 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150C VAL* 4.6 7.2 - - + -
154C MET* 4.3 22.7 - - + -
267C ILE* 3.8 26.5 - - + -
268C GLY 3.6 4.7 - - - +
269C LEU* 3.8 13.7 - - + -
351C TYR 4.4 0.2 - - - +
352C SER* 1.3 70.5 - - - +
354C MET* 1.3 55.8 + - - +
363C GLN* 3.6 2.1 - - - -
364C VAL* 2.8 42.8 + - + +
365C GLY* 2.8 25.2 + - - +
366C ILE 4.0 15.0 - - - +
367C TYR* 4.1 9.9 - - + +
372C VAL* 3.9 27.8 - - + -
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Residues in contact with MET 354 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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254C ILE* 4.7 6.5 - - + +
266C ILE 3.9 0.5 - - - +
267C ILE* 3.6 4.5 - - - +
268C GLY 2.9 38.6 + - - +
269C LEU 4.7 0.7 - - - -
270C GLN* 4.3 17.7 - - + +
352C SER* 3.7 25.4 - - - +
353C ILE* 1.3 74.2 - - - +
355C ASN* 1.3 59.8 + - - +
361C LEU* 4.5 35.8 - - + +
362C VAL 3.4 4.3 - - - -
363C GLN* 3.6 45.1 - - + +
364C VAL* 4.5 1.8 - - - -
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Residues in contact with ASN 355 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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265C GLY* 3.4 7.6 - - - +
266C ILE 2.7 23.5 - - - +
267C ILE* 3.9 12.7 - - + +
354C MET* 1.3 74.5 - - - +
356C LEU* 1.3 66.8 + - - +
357C GLN* 3.4 4.5 + - - +
361C LEU* 4.2 2.9 - - - -
362C VAL* 2.5 44.3 + - + +
364C VAL* 3.4 21.8 - - + +
378C LYS 4.6 1.0 + - - -
379C ILE* 3.8 5.3 - - - +
380C ILE* 2.9 54.4 + - - +
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Residues in contact with LEU 356 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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259C LEU* 5.7 5.4 - - + -
262C ALA* 6.0 1.3 - - + +
263C PRO 4.4 4.9 - - - +
264C ASP* 3.6 16.3 - - - +
265C GLY* 2.9 26.4 + - - +
266C ILE* 3.4 25.8 + - + +
355C ASN* 1.3 76.6 + - - +
357C GLN* 1.3 60.0 + - - +
359C ARG* 5.5 1.3 - - - -
360C LYS 3.3 10.1 - - - +
361C LEU* 4.1 15.3 - - + +
380C ILE* 5.0 0.9 - - - +
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Residues in contact with GLN 357 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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355C ASN* 3.4 5.8 + - - +
356C LEU* 1.3 72.3 - - - +
358C ASN* 1.3 75.7 + - + +
359C ARG 3.2 0.4 - - - -
360C LYS* 2.7 31.5 + - - +
362C VAL* 4.3 19.2 - - + +
380C ILE* 3.7 33.2 - - + -
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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