Contacts of the helix formed by residues 377 - 390 (chain C) in PDB entry 7C17
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 THR 377 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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711 G 4.8 22.7 - - + +
364C VAL* 4.6 4.9 - - - +
375C PRO 5.3 0.9 - - - +
376C PRO* 1.3 80.7 - - - +
378C ARG* 1.3 66.1 + - - +
379C GLU* 3.8 9.8 + - - +
380C ALA* 3.3 26.8 + - + +
381C ALA* 3.4 20.1 + - - +
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Residues in contact with ARG 378 (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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360C LEU* 3.1 44.6 - - + -
363C LEU* 5.5 0.2 - - - +
364C VAL* 5.9 1.6 - - - -
377C THR* 1.3 72.7 - - - +
379C GLU* 1.3 90.1 + - - +
381C ALA* 3.4 3.7 + - - +
382C GLU* 2.8 70.7 + - - +
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Residues in contact with GLU 379 (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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377C THR* 4.1 7.8 + - - +
378C ARG* 1.3 110.1 + - - +
380C ALA* 1.3 58.3 + - - +
382C GLU* 3.7 10.7 - - - +
383C SER* 2.9 31.2 + - - -
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Residues in contact with ALA 380 (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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711 G 6.2 4.0 - - + -
367C TYR* 3.9 11.8 - - + +
374C GLU* 5.7 2.2 - - - +
376C PRO* 4.6 6.3 - - + -
377C THR* 3.3 26.5 + - + +
379C GLU* 1.3 78.4 - - - +
381C ALA* 1.3 56.9 + - - +
383C SER* 2.8 19.6 + - - -
384C LEU* 2.9 18.9 + - - +
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Residues in contact with ALA 381 (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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363C LEU* 4.4 18.3 - - + +
364C VAL* 4.4 17.5 - - + +
366C ILE* 5.5 1.4 - - + +
367C TYR* 3.7 23.5 - - + -
376C PRO* 4.3 4.7 - - + -
377C THR 3.4 18.6 + - - +
378C ARG* 3.9 3.1 - - - +
380C ALA* 1.3 75.6 - - - +
382C GLU* 1.3 61.5 + - - +
384C LEU* 3.4 2.8 + - - +
385C PHE* 2.9 29.8 + - - +
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Residues in contact with GLU 382 (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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359C ARG* 4.4 20.3 + - - +
360C LEU* 4.6 4.6 - - + +
363C LEU* 3.7 22.9 - - + -
378C ARG* 2.8 64.7 + - + +
379C GLU* 3.7 12.2 - - - +
381C ALA* 1.3 77.7 - - - +
383C SER* 1.3 57.4 + - - +
385C PHE* 3.3 3.1 + - - +
386C GLU* 2.9 38.9 + - + +
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Residues in contact with SER 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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379C GLU 2.9 15.7 + - - -
380C ALA* 2.8 24.8 + - - -
382C GLU* 1.3 72.0 - - - +
384C LEU* 1.3 58.8 + - - +
386C GLU* 3.8 5.3 - - - +
387C ASN* 2.9 44.1 + - - +
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Residues in contact with LEU 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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366C ILE* 4.8 9.0 - - + -
367C TYR* 3.6 44.4 - - + -
370C MET* 4.5 10.5 - - + -
371C ARG* 3.7 35.9 - - + +
380C ALA 2.9 17.4 + - - +
381C ALA 3.8 4.0 - - - +
382C GLU 3.3 0.2 - - - -
383C SER* 1.3 77.7 + - - +
385C PHE* 1.3 60.2 + - - +
387C ASN* 3.7 2.8 - - - -
388C LEU* 2.9 53.1 + - + +
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Residues in contact with PHE 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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208C ILE 5.5 0.7 - - - -
209C ILE* 4.0 23.3 - - + -
212C ALA* 3.7 29.4 - - + -
213C LEU* 4.5 7.4 - - + -
363C LEU* 3.8 20.9 - - + -
366C ILE* 4.4 20.9 - - + -
381C ALA 2.9 18.3 + - - +
382C GLU* 3.3 7.4 + - - +
384C LEU* 1.3 81.2 - - + +
386C GLU* 1.3 65.1 + - - +
388C LEU* 4.6 3.4 - - - -
389C PHE* 2.9 58.3 + + - +
390C PHE* 3.6 29.6 - + - -
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Residues in contact with GLU 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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359C ARG* 5.5 4.9 + - - -
382C GLU* 2.9 25.0 + - + +
383C SER* 3.8 6.1 - - - +
384C LEU 3.3 0.2 - - - -
385C PHE* 1.3 86.5 - - - +
387C ASN* 1.3 62.9 + - - +
390C PHE* 2.9 65.1 + - - +
391C SER* 3.1 3.1 + - - -
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Residues in contact with ASN 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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383C SER* 2.9 32.3 + - - +
384C LEU* 3.7 3.1 - - - +
386C GLU* 1.3 76.3 - - - +
388C LEU* 1.3 57.2 + - - +
391C SER* 3.7 22.0 + - - +
393C ASP* 5.9 2.6 - - - +
394C ARG* 3.4 36.1 + - + +
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Residues in contact with LEU 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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182C SER* 3.0 47.3 + - - +
198C ILE* 4.1 7.6 - - + -
199C ASP* 5.7 0.2 - - - +
370C MET* 3.8 36.8 - - + -
384C LEU* 2.9 33.0 + - + +
385C PHE* 4.1 2.9 - - - +
386C GLU 3.2 0.2 - - - -
387C ASN* 1.3 80.3 - - - +
389C PHE* 1.3 88.9 + - + +
394C ARG* 5.4 3.5 - - - +
395C TYR* 4.8 7.4 - - - -
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Residues in contact with PHE 389 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
182C SER* 4.5 6.3 - - - -
184C LEU* 4.3 17.5 - - + -
198C ILE* 4.0 24.2 - - + -
209C ILE* 3.7 24.7 - - + -
366C ILE* 5.1 8.7 - - + -
385C PHE* 2.9 54.6 + + - +
388C LEU* 1.3 108.0 - - + +
390C PHE* 1.3 87.5 + + + +
391C SER 3.7 2.9 + - - -
395C TYR* 4.2 26.1 - + - -
419C ILE* 4.6 3.1 - - - +
420C LEU* 4.9 8.0 + - + +
425C ILE* 6.5 1.1 - - + -
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Residues in contact with PHE 390 (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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213C LEU* 4.2 21.8 - - + -
385C PHE* 3.6 32.1 - + - -
386C GLU* 2.9 41.8 + - - +
389C PHE* 1.3 91.9 - + + +
391C SER* 1.3 58.0 + - - +
392C GLU* 5.5 1.6 - - - +
419C ILE* 3.8 20.5 - - + +
420C LEU* 3.3 38.1 - - + -
421C SER 4.6 7.2 - - - -
422C LYS* 5.3 1.1 - - - -
425C ILE* 4.5 14.8 - - + -
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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