Contacts of the helix formed by residues 375 - 388 (chain C) in PDB entry 5D4E
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 375 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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114C PHE 3.9 6.0 + - - -
115C LEU* 3.3 38.7 - - - -
351C LEU* 4.2 8.7 - - - -
373C VAL* 3.9 4.7 + - - +
374C ASN* 1.3 73.2 + - - +
376C ARG* 1.3 66.3 + - - +
377C PRO* 3.4 0.9 - - - -
378C LEU* 2.9 17.8 + - - +
379C GLU* 2.9 30.1 + - - +
276F ARG* 5.1 1.4 - - - +
279F GLN* 3.3 22.0 + - - -
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Residues in contact with ARG 376 (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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374C ASN* 3.2 21.4 + - - +
375C SER* 1.3 77.5 - - - +
377C PRO* 1.4 62.5 - - + +
379C GLU* 2.8 40.5 + - - +
380C ALA* 2.9 30.1 + - - +
383C ARG* 5.6 0.7 + - - -
272F SER 5.2 1.8 + - - -
275F ALA* 4.5 6.7 + - - +
276F ARG* 3.7 33.5 - - - +
279F GLN* 3.5 33.2 + - - +
285F GLU* 3.9 15.6 + - - -
286F PRO* 5.8 0.2 - - - +
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Residues in contact with PRO 377 (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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347C GLY* 4.3 3.0 - - - +
350C ARG* 4.0 45.4 + - + +
351C LEU* 4.6 6.5 - - + +
374C ASN* 3.2 23.3 - - + +
376C ARG* 1.4 94.2 - - + +
378C LEU* 1.3 58.2 + - - +
380C ALA* 3.0 8.1 + - + +
381C ALA* 2.8 28.4 + - - +
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Residues in contact with LEU 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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94C LEU* 4.8 1.1 - - + -
115C LEU* 4.1 31.0 - - + +
344C PHE* 3.6 52.3 - - + +
347C GLY* 3.7 13.2 + - - +
348C LEU* 3.7 39.3 - - + +
351C LEU* 4.9 8.3 - - + -
375C SER* 2.9 10.4 + - - +
377C PRO* 1.3 76.8 - - - +
379C GLU* 1.3 68.2 + - - +
381C ALA* 2.9 12.6 + - - +
382C ILE* 3.1 16.1 + - + +
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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
----------------------------------------------------------
115C LEU 3.5 14.1 - - - +
116C GLY* 3.3 22.8 - - - -
117C HIS 4.2 9.5 + - - +
375C SER* 2.9 25.1 + - - +
376C ARG* 2.8 39.2 + - - +
378C LEU* 1.3 75.4 - - - +
380C ALA* 1.3 57.6 + - - +
382C ILE* 3.7 4.4 + - - +
383C ARG* 3.0 41.9 + - - +
279F GLN* 3.8 1.1 - - - +
285F GLU* 3.4 18.9 - - - +
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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
----------------------------------------------------------
350C ARG* 5.6 4.0 - - - +
376C ARG 2.9 18.9 + - - +
377C PRO* 3.0 10.2 + - + +
379C GLU* 1.3 74.3 - - - +
381C ALA* 1.3 59.4 + - - +
383C ARG* 4.4 16.6 - - - +
384C GLU* 3.1 27.8 + - - +
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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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343C GLN* 3.7 26.5 + - - +
346C VAL* 5.7 0.7 - - + -
347C GLY* 3.5 26.2 - - - +
350C ARG* 5.1 9.4 - - - +
377C PRO 2.8 10.9 + - - +
378C LEU 2.9 9.6 + - - +
380C ALA* 1.3 76.5 - - - +
382C ILE* 1.3 63.4 + - + +
384C GLU* 2.9 23.0 + - - +
385C PHE 3.0 9.0 + - - -
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Residues in contact with ILE 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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117C HIS 4.8 7.6 - - - +
118C ILE* 4.9 4.7 - - + -
119C PRO* 3.6 31.6 - - + -
340C MET* 3.9 26.0 - - + +
343C GLN* 4.0 7.2 - - + +
344C PHE* 3.6 52.3 - - + +
378C LEU* 3.1 13.4 + - + +
379C GLU* 4.3 3.8 - - - +
381C ALA* 1.3 78.4 - - + +
383C ARG* 1.3 61.0 + - - +
385C PHE* 2.9 19.5 + - + +
386C PHE* 3.0 22.5 + - + -
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Residues in contact with ARG 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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129C ILE* 6.3 0.2 - - + -
376C ARG 5.6 0.4 + - - -
379C GLU* 3.0 26.4 + - - +
380C ALA* 4.4 18.7 - - - +
382C ILE* 1.3 80.5 - - + +
384C GLU* 1.3 57.5 + - - +
386C PHE* 5.0 2.7 - - - -
387C SER* 2.9 48.3 + - - +
388C ARG* 4.7 13.1 - - - +
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Residues in contact with GLU 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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343C GLN* 5.1 6.3 - - - +
380C ALA 3.1 19.4 + - - +
381C ALA* 2.9 9.7 + - - +
383C ARG* 1.3 79.1 - - - +
385C PHE* 1.3 59.0 + - - +
388C ARG* 3.1 60.7 + - - +
389C SER* 3.3 9.2 + - - -
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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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136C ILE* 4.0 35.7 - - + -
336C VAL* 4.5 1.3 - - + -
339C LEU* 3.5 40.2 - - + -
340C MET* 3.7 22.4 - - + -
343C GLN* 3.5 37.7 - - + +
381C ALA 3.0 7.0 + - - +
382C ILE* 2.9 11.3 + - - +
384C GLU* 1.3 77.8 - - - +
386C PHE* 1.3 84.4 + + - +
389C SER* 3.0 36.6 - - - -
391C LEU* 5.4 4.3 - - + -
392C SER* 3.5 7.6 - - - -
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Residues in contact with PHE 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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26C TYR* 4.2 3.6 - + - -
119C PRO* 3.7 31.4 - - + -
127C PHE* 3.6 48.7 - + + -
129C ILE* 3.8 33.2 - - + -
134C ARG* 3.8 8.6 + - + -
136C ILE* 4.1 17.0 - - + -
336C VAL* 5.4 0.4 - - + -
340C MET* 3.6 32.8 - - + -
382C ILE* 3.0 29.9 + - + +
383C ARG* 4.4 2.9 - - - +
385C PHE* 1.3 86.7 - + - +
387C SER* 1.3 64.2 + - - +
392C SER* 2.4 25.8 + - - -
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Residues in contact with SER 387 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129C ILE* 3.7 19.9 - - - +
130C ASN* 5.3 6.2 + - - -
134C ARG* 3.8 20.8 + - - +
383C ARG* 2.9 29.0 + - - +
386C PHE* 1.3 80.8 - - - +
388C ARG* 1.3 81.1 + - - +
389C SER 3.9 1.6 + - - +
392C SER 5.2 0.3 - - - +
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Residues in contact with ARG 388 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
383C ARG* 4.7 16.0 + - - +
384C GLU* 3.1 45.1 + - - +
387C SER* 1.3 95.4 - - - +
389C SER* 1.3 66.3 + - - +
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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