Contacts of the strand formed by residues 370 - 375 (chain C) in PDB entry 5WWZ
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 VAL 370 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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330C GLN* 3.6 42.8 - - + +
331C VAL 3.8 6.5 - - - +
332C ARG* 3.9 28.0 - - + +
361C VAL 4.3 0.5 - - - +
363C PRO* 3.4 23.3 - - - +
368C GLU* 2.7 39.7 + - + +
369C PRO* 1.3 78.6 - - - +
371C PHE* 1.3 68.7 + - - +
372C GLU* 4.0 8.4 + - + +
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Residues in contact with PHE 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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329C VAL 3.7 0.5 - - - +
330C GLN* 3.5 4.0 - - - -
331C VAL* 2.8 48.7 + - + +
333C VAL* 3.8 29.6 - - + -
338C VAL* 4.2 9.0 - - + -
341C VAL* 3.6 34.8 - - + -
342C VAL* 4.1 16.4 - - + -
349C ILE* 4.2 7.2 - - + -
360C ILE* 3.9 20.9 - - + -
361C VAL 3.6 9.9 - - - +
362C THR* 3.8 15.3 - - - -
363C PRO* 3.7 25.8 - - + -
369C PRO 5.2 0.2 - - - -
370C VAL* 1.3 75.2 - - - +
372C GLU* 1.3 62.1 + - - +
373C VAL* 3.9 1.5 + - + -
387C ILE* 4.3 15.3 - - + -
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Residues in contact with GLU 372 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
314A HIS 5.5 4.3 + - - -
318A HIS* 6.2 2.7 - - + -
319A MET* 4.2 26.2 + - - +
328C THR* 4.4 16.8 - - + +
329C VAL 3.5 6.7 - - - +
330C GLN* 4.8 15.4 + - + +
359C TYR 3.5 2.6 - - - +
360C ILE* 3.2 3.1 - - - -
361C VAL* 2.8 54.0 + - + +
370C VAL* 4.7 13.5 - - + +
371C PHE* 1.3 73.8 - - - +
373C VAL* 1.3 62.1 + - - +
374C THR* 4.0 1.3 + - - -
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Residues in contact with VAL 373 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
327C THR 3.6 1.4 - - - +
328C THR* 3.2 3.0 - - - -
329C VAL* 3.0 39.5 + - + +
331C VAL* 3.8 24.9 - - + -
358C THR* 3.9 6.1 - - - -
359C TYR 3.5 2.2 - - - -
360C ILE* 3.8 23.8 - - + -
371C PHE 4.4 2.5 - - - +
372C GLU* 1.3 75.1 - - - +
374C THR* 1.3 63.2 + - - +
380C VAL* 3.8 23.6 - - + +
383C ALA* 3.7 26.5 - - + -
384C ARG 5.3 0.7 - - - +
387C ILE* 4.1 14.6 - - + -
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Residues in contact with THR 374 (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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318A HIS* 3.5 17.7 - - + +
322C ASN* 3.6 21.8 - - + +
326C GLN* 4.2 13.5 - - + +
327C THR 3.2 5.2 - - - +
328C THR* 2.8 33.1 + - - +
358C THR* 3.4 5.4 - - - -
359C TYR* 2.6 58.3 + - + +
361C VAL* 6.1 0.2 - - - +
372C GLU* 4.6 1.9 + - - +
373C VAL* 1.3 71.9 - - - +
375C GLY* 1.3 61.5 + - - +
380C VAL* 3.8 3.6 - - - -
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Residues in contact with GLY 375 (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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326C GLN* 3.8 22.4 - - - +
327C THR* 2.9 29.5 + - - +
357C HIS 4.9 4.9 - - - -
358C THR* 4.7 5.4 - - - -
374C THR* 1.3 78.7 - - - +
376C MET* 1.3 68.8 + - - +
377C PRO 3.6 0.3 - - - -
380C VAL* 3.4 7.0 - - - +
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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