Contacts of the strand formed by residues 382 - 389 (chain C) in PDB entry 5E1T
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 382 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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325C PHE* 3.7 6.1 - - - -
326C ILE* 2.8 41.4 + - - +
362C PHE* 3.9 7.3 - - - -
370C SER* 3.4 26.9 - - - -
371C PHE* 3.5 25.1 - - - -
380C VAL 3.8 0.2 + - - -
381C ALA* 1.3 75.7 - - - +
383C GLY* 1.3 62.0 + - - +
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Residues in contact with GLY 383 (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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324C LEU 3.9 3.6 - - - -
325C PHE* 3.4 9.3 - - - -
347C PHE* 4.4 1.6 - - - -
362C PHE* 3.8 21.9 - - - -
382C SER* 1.3 80.7 + - - +
384C CYS* 1.3 66.1 + - - +
385C PRO* 3.4 12.9 - - - +
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Residues in contact with CYS 384 (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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323C SER* 3.9 0.2 - - - -
324C LEU 2.9 28.0 + - - +
325C PHE* 4.0 1.5 - - - -
347C PHE* 3.9 19.1 - - + -
360C ASP* 3.8 30.7 - - - +
361C ALA 5.0 3.4 - - - -
362C PHE* 4.6 11.9 - - - -
383C GLY* 1.3 77.0 - - - -
385C PRO* 1.3 69.2 - - - +
386C LEU 3.6 0.2 + - - -
387C PHE* 3.1 34.3 + - + +
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Residues in contact with PRO 385 (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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314C ASP* 4.2 6.7 - - - +
316C THR* 3.3 28.9 - - - +
323C SER* 3.7 17.5 - - - +
325C PHE* 3.9 17.4 - - + -
383C GLY 3.4 9.0 - - - +
384C CYS* 1.3 94.5 - - - +
386C LEU* 1.3 70.3 + - + +
387C PHE* 4.2 0.2 - - - -
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Residues in contact with LEU 386 (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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316C THR* 3.2 38.2 + - - +
317C GLY* 3.6 7.2 - - - +
320C THR* 4.3 0.4 - - - +
321C HIS* 3.3 55.3 + - + +
322C LEU 3.9 1.4 + - - -
323C SER* 4.2 1.4 + - - -
360C ASP* 5.3 1.7 - - - +
385C PRO* 1.3 75.5 - - + +
387C PHE* 1.3 63.5 + - - +
388C PHE* 3.3 3.2 + - - -
389C PRO* 5.6 0.2 - - - +
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Residues in contact with PHE 387 (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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309C LEU* 6.3 0.2 - - + -
322C LEU* 3.1 17.4 + - + +
324C LEU* 4.0 24.9 - - + -
347C PHE* 3.4 40.2 - + + -
348C MET 3.9 0.9 - - - -
349C LEU* 3.5 42.4 - - + -
358C ALA* 3.6 12.8 - - + +
360C ASP* 3.9 26.0 - - + +
384C CYS* 3.1 28.5 - - + +
385C PRO 3.2 2.1 - - - -
386C LEU* 1.3 77.7 - - - +
388C PHE* 1.3 72.8 + - + +
408C LEU* 4.2 6.3 - - + -
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Residues in contact with PHE 388 (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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321C HIS* 3.2 7.8 - - - -
322C LEU* 2.8 41.1 + - + +
349C LEU* 3.8 14.4 - - + -
358C ALA* 3.7 31.0 - - + -
386C LEU 3.3 1.0 - - - -
387C PHE* 1.3 91.9 - - + +
389C PRO* 1.3 95.7 - - + +
392C LYS* 3.8 16.8 - - + -
393C LEU* 3.7 30.5 - - + -
400C TYR* 3.2 38.4 - + - -
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Residues in contact with PRO 389 (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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320C THR 3.8 6.5 - - - +
321C HIS* 3.8 16.8 - - + +
322C LEU* 5.8 0.2 - - - -
386C LEU 5.6 0.2 - - - +
388C PHE* 1.3 104.7 - - + +
390C LEU* 1.3 66.6 + - - +
391C SER* 3.2 18.1 + - - +
392C LYS* 3.8 18.6 - - + +
393C LEU* 3.3 16.6 + - - +
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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