Contacts of the helix formed by residues 346 - 361 (chain C) in PDB entry 5A31
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 GLN 346 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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341C TYR* 3.0 42.7 + - + +
344C ARG* 3.1 50.6 + - - +
345C SER* 1.3 75.5 - - - +
347C HIS* 1.3 64.1 + - - +
348C GLU* 3.4 5.6 + - + +
349C LYS* 3.6 16.3 + - + +
350C ALA* 3.2 16.3 + - - +
25M PRO* 5.0 3.0 - - - +
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Residues in contact with HIS 347 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
342C SER* 3.6 26.4 + - - -
345C SER* 3.4 27.7 + - - -
346C GLN* 1.3 72.2 - - - +
348C GLU* 1.3 72.2 + - - +
350C ALA* 3.5 2.5 - - - +
351C ALA* 2.9 25.8 + - - +
374C GLU* 3.0 34.4 + - - +
377C GLU* 3.4 43.6 + - + +
378C MET* 3.8 21.8 - - + +
64R ILE* 5.5 2.9 - - + +
126R GLY 5.5 1.8 - - - -
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Residues in contact with GLU 348 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
346C GLN* 3.4 3.6 - - + -
347C HIS* 1.3 82.7 + - - +
349C LYS* 1.3 68.3 + - + +
351C ALA* 3.2 4.3 + - - +
352C LEU* 3.1 20.8 + - - +
378C MET* 2.9 36.4 - - - +
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Residues in contact with LYS 349 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
341C TYR* 3.6 49.8 - - + +
346C GLN* 3.6 18.3 + - + +
347C HIS 3.2 0.4 - - - -
348C GLU* 1.3 81.1 - - + +
350C ALA* 1.3 65.5 + - - +
352C LEU* 3.0 20.7 + - - +
353C TYR* 3.0 44.8 + - - -
356C ARG* 5.6 0.4 - - - +
22M ASP* 4.1 16.3 + - - -
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Residues in contact with ALA 350 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
338C GLY* 3.6 23.5 - - - +
341C TYR* 3.9 7.6 - - - +
342C SER* 3.7 13.7 - - - +
346C GLN 3.2 11.6 + - - +
347C HIS* 3.2 9.9 + - - +
349C LYS* 1.3 74.8 - - - +
351C ALA* 1.3 68.5 + - - +
352C LEU 3.2 0.2 + - - -
353C TYR* 3.3 3.3 + - - +
354C PHE* 2.9 28.2 + - + -
374C GLU* 3.8 17.9 - - + -
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Residues in contact with ALA 351 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
347C HIS 2.9 12.8 + - - +
348C GLU 3.5 9.2 - - - +
350C ALA* 1.3 75.9 - - - +
352C LEU* 1.3 59.0 + - - +
354C PHE* 3.1 8.4 + - - +
355C GLN* 2.9 29.5 + - - +
371C MET* 4.4 6.0 - - - +
374C GLU* 4.2 16.8 - - + +
375C TYR* 4.0 35.9 - - + +
378C MET* 4.6 3.6 - - + -
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Residues in contact with LEU 352 (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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348C GLU 3.1 9.7 + - - +
349C LYS* 3.0 24.0 + - - +
351C ALA* 1.3 81.2 - - - +
353C TYR* 1.3 63.6 + - + +
355C GLN* 3.2 18.0 - - + +
356C ARG* 2.9 74.2 + - + +
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Residues in contact with TYR 353 (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 CYS* 6.6 0.2 - - - -
334C CYS* 3.6 35.7 - - - +
337C ILE* 3.3 30.3 - - + -
338C GLY* 3.9 13.2 - - - -
341C TYR* 3.8 23.2 + + - -
349C LYS* 3.0 33.6 + - - +
350C ALA 3.3 0.4 + - - -
352C LEU* 1.3 74.5 - - + +
354C PHE* 1.3 60.7 + - - +
356C ARG* 3.2 30.7 + - - +
357C ALA* 2.9 27.9 + - - +
19M TRP* 4.4 9.8 - + - -
22M ASP* 3.2 28.9 + - - +
23M LYS 5.9 0.2 - - - -
24M LEU* 5.8 1.8 - - + +
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Residues in contact with PHE 354 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
335C CYS* 4.0 29.4 - - + -
338C GLY* 3.6 26.2 - - - -
339C ASN* 3.6 4.0 - - - -
350C ALA 2.9 24.0 + - - -
351C ALA* 3.1 7.2 + - - +
353C TYR* 1.3 75.7 - - - +
355C GLN* 1.3 65.2 + - - +
357C ALA* 3.2 6.2 + - - +
358C LEU* 3.1 19.4 + - - +
367C ALA* 3.7 16.8 - - + +
370C LEU* 3.4 36.3 - - + -
371C MET* 4.0 22.2 - - + -
374C GLU* 3.7 28.9 - - + -
47R ARG* 3.6 16.6 - - - -
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Residues in contact with GLN 355 (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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351C ALA 2.9 12.2 + - - +
352C LEU* 3.2 21.7 - - + +
354C PHE* 1.3 74.2 - - - +
356C ARG* 1.3 64.7 + - + +
358C LEU* 3.2 7.5 + - + +
359C LYS* 3.1 30.5 + - - +
371C MET* 3.0 33.1 - - + +
375C TYR* 3.0 15.2 + - - -
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Residues in contact with ARG 356 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
334C CYS* 4.1 2.5 - - - -
349C LYS* 5.6 0.6 - - - +
352C LEU* 2.9 48.2 + - + +
353C TYR* 3.2 42.4 + - - +
354C PHE 3.3 0.2 - - - -
355C GLN* 1.3 77.3 - - + +
357C ALA* 1.3 63.7 + - - +
359C LYS* 3.1 17.9 + - - +
360C LEU* 3.1 24.3 + - - +
16M ASP* 5.6 0.6 + - - -
18M ALA* 4.2 4.6 + - - +
19M TRP* 3.2 83.1 - - + +
22M ASP* 4.0 8.7 + - - -
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Residues in contact with ALA 357 (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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331C VAL* 3.5 26.3 - - + +
334C CYS* 3.8 20.9 - - + -
335C CYS* 4.1 17.3 - - + +
353C TYR 2.9 17.4 + - - +
354C PHE* 3.5 8.7 - - - +
355C GLN 3.2 0.2 - - - -
356C ARG* 1.3 75.2 - - - +
358C LEU* 1.3 62.6 + - - +
360C LEU* 3.2 13.1 + - - +
361C ASN* 3.4 8.5 + - - +
364C TYR* 4.8 0.2 - - + -
367C ALA* 4.4 7.4 - - + -
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Residues in contact with LEU 358 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141C LEU* 4.5 8.3 - - + -
354C PHE 3.1 10.8 + - - +
355C GLN* 3.5 9.2 - - - +
356C ARG 3.0 0.2 - - - -
357C ALA* 1.3 76.2 - - - +
359C LYS* 1.3 57.6 + - - +
361C ASN* 3.1 2.0 + - - +
362C PRO* 2.6 44.8 - - - +
364C TYR* 3.0 31.4 - - - +
367C ALA* 3.6 9.2 - - + -
368C TRP* 3.1 73.8 - - + +
371C MET* 4.2 11.0 - - + -
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Residues in contact with LYS 359 (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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141C LEU* 4.4 17.0 - - + +
355C GLN* 3.1 15.5 + - - +
356C ARG* 3.3 29.1 - - - +
358C LEU* 1.3 80.8 - - - +
360C LEU* 1.3 60.6 + - - +
361C ASN 3.5 0.9 + - - -
362C PRO* 4.3 7.6 - - - +
14M LEU* 3.3 37.3 + - + +
16M ASP* 4.3 15.2 + - - -
19M TRP* 4.4 11.6 - - + -
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Residues in contact with LEU 360 (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 TYR* 4.1 4.5 - - + -
330C ARG* 3.8 39.7 - - - +
331C VAL* 4.1 10.1 - - + +
334C CYS* 4.5 4.0 - - + -
356C ARG 3.1 16.8 + - - +
357C ALA 3.2 6.7 + - - +
359C LYS* 1.3 78.4 - - - +
361C ASN* 1.4 62.7 + - - +
10M ARG* 4.7 13.7 + - - -
11M ILE* 5.7 5.2 - - + -
14M LEU* 3.7 29.3 - - + +
15M ILE* 4.9 7.2 - - + -
19M TRP* 3.6 35.0 - - + -
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Residues in contact with ASN 361 (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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331C VAL* 3.9 27.7 - - - +
357C ALA 3.4 4.8 + - - +
358C LEU 3.1 7.2 + - - +
360C LEU* 1.4 83.9 + - - +
362C PRO* 1.3 60.3 - - + +
363C ARG* 3.2 36.0 + - - +
364C TYR* 3.5 23.2 + - + +
10M ARG* 5.7 1.9 + - - -
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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