Contacts of the strand formed by residues 365 - 372 (chain C) in PDB entry 3P3W
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 365 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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233C MET* 6.2 0.2 - - - -
359C GLU 3.8 6.3 - - - -
360C MET* 3.9 29.6 - - - -
361C LYS 4.6 1.3 - - - +
364C GLY* 1.3 72.6 - - - -
366C ARG* 1.3 63.4 + - - +
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Residues in contact with ARG 366 (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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358C TYR* 3.5 13.9 - - - -
359C GLU* 3.2 42.0 + - + +
361C LYS* 4.6 24.6 - - + +
364C GLY* 5.1 6.7 - - - +
365C SER* 1.3 77.2 - - - +
367C LYS* 1.3 68.6 + - - +
368C ALA* 4.9 13.8 + - - +
379C PRO 5.2 6.7 + - - -
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Residues in contact with LYS 367 (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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246C ASN* 4.1 18.0 + - - +
248C GLU* 4.6 14.3 - - + +
356C ASP* 3.3 38.5 + - + -
357C VAL 4.2 6.5 - - - +
358C TYR* 4.0 31.3 + - + +
366C ARG* 1.3 81.5 + - - +
368C ALA* 1.3 64.3 + - - +
369C GLY* 4.3 13.4 - - - +
370C TYR* 5.8 1.1 - - - -
380C PHE* 6.2 2.4 - - - -
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Residues in contact with ALA 368 (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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128C TYR* 6.1 0.9 - - - +
357C VAL* 3.2 24.3 + - + +
359C GLU* 4.5 19.1 - - + +
366C ARG* 3.7 18.1 + - - +
367C LYS* 1.3 73.6 - - - +
369C GLY* 1.3 58.5 + - - +
377C PHE* 4.8 11.2 - - + -
379C PRO* 3.0 30.8 - - + +
380C PHE* 4.8 1.6 - - - +
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Residues in contact with GLY 369 (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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356C ASP* 3.7 5.6 - - - +
357C VAL* 3.0 29.4 + - - +
367C LYS* 3.4 12.2 - - - +
368C ALA* 1.3 82.6 - - - +
370C TYR* 1.3 62.2 + - - -
377C PHE* 4.8 3.6 - - - -
378C VAL 3.2 12.8 - - - -
379C PRO* 4.4 0.9 - - - -
380C PHE* 4.7 10.8 - - - -
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Residues in contact with TYR 370 (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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354C THR* 3.8 21.5 - - + -
355C ILE 3.3 7.0 - - - +
356C ASP* 4.0 10.5 - - - +
357C VAL* 5.2 0.4 - - - -
367C LYS* 5.8 0.7 - - - -
369C GLY* 1.3 74.4 - - - +
371C TRP* 1.3 62.2 + - - +
372C ASN* 3.4 30.3 - - - -
375C GLU* 2.7 25.6 + - - -
377C PHE* 3.9 4.0 - - - -
378C VAL* 3.1 57.9 + - + +
380C PHE* 3.6 34.8 - + - -
176D ARG* 5.8 1.5 + - - -
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Residues in contact with TRP 371 (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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119C GLY* 3.8 29.2 - - - -
120C ALA* 4.0 21.0 - - + +
123C SER* 3.8 20.6 + - - -
124C LEU* 6.3 1.6 - - + -
353C TYR* 3.5 25.8 - + - -
354C THR* 3.4 3.6 - - - -
355C ILE* 2.7 61.0 + - + +
357C VAL* 4.9 7.2 - - + -
370C TYR* 1.3 76.3 - - - +
372C ASN* 1.3 78.5 + - - +
373C GLU* 3.8 27.8 - - + -
376C ARG* 2.4 40.0 + - - +
377C PHE* 3.5 17.0 - + + -
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Residues in contact with ASN 372 (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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352C ASN* 5.5 2.2 - - - -
353C TYR 3.2 23.3 - - - +
354C THR* 4.3 6.2 + - + +
370C TYR* 3.4 25.7 - - - -
371C TRP* 1.3 88.8 - - - +
373C GLU* 1.3 67.1 + - - +
374C TYR* 3.5 9.9 + - + +
375C GLU* 2.4 54.0 + - - +
376C ARG 3.1 18.7 + - - -
176D ARG* 5.5 3.0 - - - +
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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