Contacts of the helix formed by residues 320 - 335 (chain Y) 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 320 (chain Y).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62F LYS* 6.1 0.2 - - - +
291Y VAL* 4.0 15.0 - - - +
295Y GLU* 2.8 33.1 + - - -
311Y TYR* 5.0 0.2 + - - -
315Y LEU* 3.1 23.1 + - + +
316Y ALA* 5.8 0.2 - - - -
318Y GLU* 3.7 24.7 - - + +
319Y GLY* 1.3 73.8 - - - +
321Y LEU* 1.3 65.4 + - - +
322Y GLU* 3.2 3.4 + - - +
323Y ASP* 3.0 38.8 + - + +
324Y VAL* 3.4 22.4 + - - +
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Residues in contact with LEU 321 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
316Y ALA* 5.7 3.8 - - + -
319Y GLY* 3.1 13.4 + - - +
320Y ARG* 1.3 75.3 - - - +
322Y GLU* 1.3 57.8 + - + +
324Y VAL* 3.1 10.0 + - + +
325Y GLU* 2.9 25.8 + - - +
348Y HIS* 3.6 39.6 - - + +
351Y TYR* 3.4 47.3 - - + +
352Y SER* 4.4 7.4 - - - +
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Residues in contact with GLU 322 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81E LYS* 4.4 20.5 - - - +
557H LYS* 4.8 11.3 + - - +
561H ASP* 4.6 9.5 - - - +
320Y ARG* 3.2 1.4 - - - +
321Y LEU* 1.3 74.9 - - + +
323Y ASP* 1.3 65.7 + - - +
325Y GLU* 3.2 7.2 + - - +
326Y ASN* 2.9 38.2 + - - +
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Residues in contact with ASP 323 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
295Y GLU* 4.5 2.8 - - - +
311Y TYR* 5.5 1.6 + - - +
315Y LEU* 3.5 22.1 - - + +
320Y ARG* 3.0 57.9 + - + +
321Y LEU 3.3 0.2 - - - -
322Y GLU* 1.3 79.6 - - - +
324Y VAL* 1.3 53.1 + - - +
326Y ASN* 3.4 7.4 + - - +
327Y LEU* 2.8 36.0 + - - +
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Residues in contact with VAL 324 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
312Y GLY* 3.9 12.8 - - - +
315Y LEU* 3.5 30.5 - - + -
316Y ALA* 4.3 9.2 - - + +
320Y ARG 3.4 7.8 + - - +
321Y LEU* 3.1 12.0 + - + +
323Y ASP* 1.3 76.9 - - - +
325Y GLU* 1.3 56.4 + - - +
327Y LEU* 3.7 6.0 - - - +
328Y GLY* 2.8 27.0 + - - -
344Y VAL* 3.7 20.5 - - + +
347Y CYS* 4.6 2.2 - - + -
348Y HIS* 3.5 38.6 - - + +
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Residues in contact with GLU 325 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73E ASP* 4.4 12.8 - - - +
74E GLN* 4.1 34.7 + - + +
77E ALA* 5.1 8.1 - - - +
557H LYS* 5.7 4.7 + - - +
321Y LEU 2.9 11.8 + - - +
322Y GLU* 3.2 9.4 + - - +
324Y VAL* 1.3 75.1 - - - +
326Y ASN* 1.3 59.8 + - - +
328Y GLY* 3.8 1.0 - - - -
329Y CYS* 3.0 36.6 + - - -
348Y HIS* 3.0 44.5 + - + +
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Residues in contact with ASN 326 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
554H VAL* 6.4 0.2 - - - +
557H LYS* 3.4 31.5 + - - +
558H ASP* 5.3 11.9 + - - +
561H ASP* 5.9 0.2 + - - -
322Y GLU* 2.9 23.7 + - - +
323Y ASP* 3.6 6.7 - - - +
325Y GLU* 1.3 73.1 - - - +
327Y LEU* 1.3 60.1 + - - +
329Y CYS* 3.4 7.3 + - - +
330Y ARG* 2.9 59.0 + - - +
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Residues in contact with LEU 327 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
298Y GLN* 3.5 32.1 - - - +
308Y MET* 3.9 29.2 - - + +
311Y TYR* 3.4 32.3 - - + -
312Y GLY* 4.3 9.2 - - - +
315Y LEU* 4.5 4.3 - - + -
323Y ASP 2.8 22.3 + - - +
324Y VAL* 3.7 5.4 - - - +
326Y ASN* 1.3 73.4 - - - +
328Y GLY* 1.3 51.7 + - - +
330Y ARG* 3.4 6.9 + - + +
331Y LEU* 2.8 40.3 + - + +
344Y VAL* 3.9 19.3 - - + -
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Residues in contact with GLY 328 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74E GLN* 5.3 3.4 - - - -
324Y VAL 2.8 19.9 + - - -
325Y GLU* 3.8 2.2 - - - -
326Y ASN 3.3 0.2 - - - -
327Y LEU* 1.3 69.6 - - - +
329Y CYS* 1.3 64.9 + - - +
331Y LEU* 3.2 1.9 + - - +
332Y PHE* 3.0 34.3 + - - -
344Y VAL* 3.7 22.6 - - - +
345Y SER* 4.5 8.7 - - - -
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Residues in contact with CYS 329 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71E LYS* 6.1 1.6 - - - +
74E GLN* 3.1 28.8 - - - +
78E ARG* 3.0 32.8 - - - +
554H VAL* 5.5 5.4 - - + -
325Y GLU* 3.0 26.5 + - - +
326Y ASN* 3.6 7.0 - - - +
328Y GLY* 1.3 71.9 - - - +
330Y ARG* 1.3 67.9 + - + +
332Y PHE* 3.4 4.5 + - - +
333Y ASN* 3.0 37.5 + - - +
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Residues in contact with ARG 330 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
530H ASN* 5.1 10.5 - - - +
554H VAL* 6.5 1.3 - - + -
558H ASP* 5.4 7.4 + - - -
298Y GLN* 3.7 38.9 + - - +
299Y MET* 5.9 3.8 - - - +
302Y PRO 5.8 4.9 - - - +
326Y ASN* 2.9 49.3 + - - +
327Y LEU* 3.7 6.1 - - + +
329Y CYS* 1.3 76.6 - - + +
331Y LEU* 1.3 59.2 + - + +
333Y ASN* 3.8 5.5 - - - +
334Y ILE* 3.0 39.5 + - + +
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Residues in contact with LEU 331 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
304Y LEU 5.4 0.4 - - - +
305Y ILE* 4.3 12.6 - - + +
308Y MET* 3.6 42.0 - - + -
327Y LEU* 2.8 21.6 + - + +
328Y GLY 3.6 4.7 - - - +
329Y CYS 3.2 0.2 - - - -
330Y ARG* 1.3 76.3 - - + +
332Y PHE* 1.3 60.0 + - - +
334Y ILE* 3.1 22.6 - - + +
335Y SER* 2.8 27.1 + - - +
340Y GLU* 3.9 11.0 - - + +
341Y PRO* 3.8 29.6 - - + +
344Y VAL* 3.5 27.6 - - + -
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Residues in contact with PHE 332 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67E LEU* 3.4 30.7 - - + -
70E VAL* 4.9 6.1 - - + -
71E LYS* 3.4 34.5 - - - +
74E GLN* 5.9 2.7 - - - -
328Y GLY 3.0 26.4 + - - +
329Y CYS* 4.0 4.0 - - - +
331Y LEU* 1.3 76.7 - - - +
333Y ASN* 1.3 62.5 + - - +
335Y SER 2.8 19.4 + - - +
336Y ASP* 3.5 27.4 - - - +
341Y PRO* 3.6 30.7 - - + -
342Y TRP* 3.8 20.6 - + - -
345Y SER* 3.2 25.8 - - - -
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Residues in contact with ASN 333 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71E LYS* 5.3 5.2 + - - -
527H ARG* 5.7 3.7 + - - +
550H VAL* 6.4 0.4 - - - +
551H ALA* 6.0 3.0 - - - +
554H VAL* 5.0 15.2 - - - +
94X ARG* 3.9 16.1 + - - -
329Y CYS* 3.0 24.9 + - - +
330Y ARG* 3.8 6.1 - - - +
332Y PHE* 1.3 77.2 - - - +
334Y ILE* 1.3 69.7 + - + +
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Residues in contact with ILE 334 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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527H ARG* 4.5 11.9 - - - +
94X ARG* 2.5 35.5 + - + +
149X LEU* 5.3 1.6 - - - +
302Y PRO* 4.4 8.5 - - + +
303Y TYR* 3.4 53.8 - - + -
304Y LEU 4.9 0.2 - - - +
305Y ILE* 3.8 23.1 - - + -
330Y ARG* 3.0 24.0 + - + +
331Y LEU* 3.1 29.4 - - + +
333Y ASN* 1.3 77.8 - - + +
335Y SER* 1.3 75.4 + - - +
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Residues in contact with SER 335 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92X GLU* 6.0 3.6 - - - -
93X TYR 6.0 1.6 - - - -
94X ARG* 5.5 2.2 - - - -
149X LEU* 6.4 0.9 - - - -
305Y ILE* 3.2 26.2 - - - +
331Y LEU 2.8 19.2 + - - +
332Y PHE* 2.8 16.6 - - - +
333Y ASN 3.3 1.8 - - - -
334Y ILE* 1.3 89.5 - - - +
336Y ASP* 1.3 62.1 + - - +
338Y HIS* 3.3 20.2 - - - -
341Y PRO* 4.2 6.6 - - - +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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