Contacts of the helix formed by residues 330 - 345 (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 ARG 330 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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297C ILE* 3.2 32.1 - - + +
298C GLU* 4.9 4.4 - - - +
327C ASP* 3.4 39.8 + - + +
328C LYS 3.6 2.0 + - - -
329C TYR* 1.3 79.3 - - - +
331C VAL* 1.3 69.0 + - - +
332C GLU* 3.1 32.9 + - - +
333C THR* 2.9 20.3 - - + +
334C CYS* 3.1 8.1 + - - +
360C LEU* 3.8 8.4 - - - +
96P VAL* 5.9 1.8 - - - +
98P GLU* 4.1 21.2 + - - -
101P ARG* 5.4 1.2 - - - +
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Residues in contact with VAL 331 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
301C ASP* 3.7 4.3 - - - +
330C ARG* 1.3 76.2 - - + +
332C GLU* 1.3 89.0 + - + +
334C CYS* 3.1 13.1 + - - +
335C CYS* 3.1 9.0 + - - +
357C ALA* 3.5 25.1 - - + +
360C LEU* 4.1 14.3 - - + +
361C ASN* 3.9 27.8 - - - +
364C TYR* 3.7 28.7 - - + -
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Residues in contact with GLU 332 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
297C ILE* 3.4 30.3 - - + +
298C GLU* 3.1 24.4 - - - +
300C MET* 5.0 1.3 - - + -
301C ASP* 3.5 33.2 - - + +
323C LEU* 4.9 0.2 - - - -
330C ARG* 3.1 28.0 + - - +
331C VAL* 1.3 99.2 + - + +
333C THR* 1.3 64.1 - - - +
335C CYS 3.2 0.7 + - - -
336C VAL* 3.0 22.4 + - - +
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Residues in contact with THR 333 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
297C ILE* 4.5 4.6 - - - +
323C LEU* 3.8 33.4 - - - +
324C CYS* 4.1 7.8 + - - -
327C ASP 2.8 29.0 + - - +
328C LYS* 3.3 17.5 + - - +
330C ARG* 2.9 28.5 - - + +
332C GLU* 1.3 80.1 - - - +
334C CYS* 1.3 57.3 + - - +
336C VAL* 2.9 1.9 + - - +
337C ILE* 2.8 43.5 + - - +
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Residues in contact with CYS 334 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
328C LYS 4.2 12.6 - - - -
330C ARG 3.1 9.8 + - - +
331C VAL 3.1 6.1 + - - +
333C THR* 1.3 77.2 - - - +
335C CYS* 1.3 57.6 + - - +
337C ILE* 3.7 5.2 + - - +
338C GLY* 3.0 21.0 + - - -
353C TYR* 3.6 36.7 - - - +
356C ARG* 4.1 5.4 - - - -
357C ALA* 3.8 22.0 - - + -
360C LEU* 4.5 2.7 - - + -
19M TRP* 3.3 37.0 - - - -
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Residues in contact with CYS 335 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
301C ASP* 2.1 45.5 - - - +
305C ASN* 4.9 0.9 - - - -
331C VAL 3.1 7.6 + - - +
333C THR 3.1 0.2 - - - -
334C CYS* 1.3 76.6 - - - +
336C VAL* 1.3 63.8 + - - +
338C GLY* 3.6 0.7 - - - +
339C ASN* 2.8 36.0 + - - -
354C PHE* 4.0 20.0 - - + -
357C ALA* 4.1 7.8 - - + +
364C TYR* 3.9 22.4 - - + -
370C LEU* 4.4 6.1 - - - -
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Residues in contact with VAL 336 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
300C MET 3.8 15.3 - - - +
301C ASP* 4.4 0.9 - - - +
304C SER* 3.5 29.1 + - - -
316C LEU* 4.4 5.6 - - + +
319C LEU* 4.0 13.2 - - + -
320C ALA* 3.7 31.6 - - + +
323C LEU* 3.6 26.9 - - + -
332C GLU 3.0 12.7 + - - +
333C THR 2.9 8.3 + - - +
335C CYS* 1.3 76.0 - - - +
337C ILE* 1.3 60.2 + - + +
339C ASN* 3.1 3.6 + - - +
340C TYR* 2.9 26.2 + - - +
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Residues in contact with ILE 337 (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 ALA* 3.7 17.5 - - + +
324C CYS* 4.1 12.6 - - + -
333C THR* 2.8 30.6 + - - +
334C CYS* 3.7 5.6 - - - +
336C VAL* 1.3 79.7 - - + +
338C GLY* 1.3 55.7 + - - +
340C TYR* 3.4 7.2 - - - +
341C TYR* 3.1 39.4 + - + -
353C TYR* 3.3 41.1 - - + -
24M LEU* 3.5 36.1 - - + -
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Residues in contact with GLY 338 (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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334C CYS 3.0 16.4 + - - -
335C CYS 3.1 3.5 + - - -
337C ILE* 1.3 72.8 - - - +
339C ASN* 1.3 63.7 + - - +
341C TYR 3.2 2.1 + - - -
342C SER* 3.0 19.2 + - - -
350C ALA* 3.6 16.5 - - - +
353C TYR* 3.9 14.1 - - - -
354C PHE* 3.6 20.4 - - - -
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Residues in contact with ASN 339 (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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304C SER* 2.8 31.4 + - - +
305C ASN* 3.2 24.5 + - - +
308C TYR* 3.7 19.6 - - + -
316C LEU* 4.2 5.6 - - + -
335C CYS* 2.8 28.0 + - - -
336C VAL 3.4 3.1 - - - +
338C GLY* 1.3 70.5 - - - +
340C TYR* 1.3 62.9 + - - +
342C SER* 2.9 22.2 + - - -
343C LEU* 3.1 6.2 + - - +
354C PHE* 3.6 4.8 - - - -
370C LEU* 5.0 0.2 - - - +
47R ARG* 2.9 40.1 + - - +
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Residues in contact with TYR 340 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
313C LYS* 5.7 2.0 - - + -
316C LEU* 3.7 17.0 - - + +
317C SER* 3.1 42.8 - - - -
320C ALA* 4.0 17.0 - - + -
321C HIS* 3.6 9.2 + + - -
336C VAL 2.9 13.2 + - - +
337C ILE 3.4 11.9 - - - +
338C GLY 3.3 0.2 - - - -
339C ASN* 1.3 76.7 - - - +
341C TYR* 1.3 70.4 + + - +
343C LEU* 3.4 3.1 + - - +
344C ARG* 3.1 41.0 + - + +
24M LEU* 3.6 29.8 - - + -
25M PRO* 3.5 26.5 + - + +
27M GLU* 3.4 25.1 - - - +
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Residues in contact with TYR 341 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
337C ILE* 3.1 34.2 + - + +
338C GLY* 3.2 4.5 + - - +
340C TYR* 1.3 83.8 - + - +
342C SER* 1.3 66.4 + - - +
343C LEU 3.1 0.4 - - - -
344C ARG* 3.3 3.1 + - - +
345C SER 3.0 16.6 + - - -
346C GLN* 3.0 51.7 + - + +
349C LYS* 3.6 41.5 - - + +
350C ALA* 3.9 7.9 - - - -
353C TYR* 3.8 28.1 + + - -
22M ASP* 4.9 2.8 + - - -
23M LYS 4.5 3.5 + - - -
24M LEU* 3.7 17.4 - - + +
25M PRO* 3.3 28.6 - - + +
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Residues in contact with SER 342 (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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308C TYR* 3.1 24.6 + - - -
338C GLY 3.0 11.8 + - - -
339C ASN 2.9 16.8 + - - -
341C TYR* 1.3 77.5 - - - +
343C LEU* 1.3 57.2 + - - +
345C SER* 3.1 17.5 + - - -
347C HIS* 3.6 13.0 + - - -
350C ALA* 3.7 6.3 - - - +
374C GLU* 3.3 35.2 - - - -
47R ARG* 3.1 12.0 + - - -
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Residues in contact with LEU 343 (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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308C TYR* 3.4 44.6 - - + +
311C SER* 4.5 25.6 - - - +
312C MET 4.8 0.4 - - - +
313C LYS* 3.7 39.1 + - + +
316C LEU* 3.5 23.3 - - + -
339C ASN 3.1 8.6 + - - +
340C TYR 3.7 9.0 - - - +
341C TYR 3.1 0.6 - - - -
342C SER* 1.3 76.0 + - - +
344C ARG* 1.3 61.1 + - - +
345C SER* 3.0 7.2 + - - -
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Residues in contact with ARG 344 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
313C LYS* 4.4 10.3 - - + +
340C TYR* 3.1 35.7 + - + +
341C TYR* 3.3 6.3 + - - +
343C LEU* 1.3 73.4 - - - +
345C SER* 1.3 68.4 + - - +
346C GLN* 3.1 33.7 + - - +
25M PRO* 3.5 29.8 - - - +
26M TYR 4.3 5.3 + - - -
27M GLU* 3.2 52.2 + - - +
28M ASP* 4.7 5.7 + - - +
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Residues in contact with SER 345 (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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341C TYR 3.0 3.4 + - - -
342C SER 3.4 13.2 - - - -
343C LEU 3.0 6.8 - - - -
344C ARG* 1.3 81.5 - - - +
346C GLN* 1.3 62.2 + - - +
347C HIS* 3.4 27.5 + - - -
125R LYS* 5.6 4.3 + - - -
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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