Contacts of the helix formed by residues 328 - 344 (chain A) in PDB entry 1YQS
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 ASN 328 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21A GLN 2.9 24.8 + - - +
22A GLY* 4.0 8.9 - - - -
215A THR* 3.8 23.0 + - - +
306A TYR* 2.9 12.2 + - + -
325A THR* 4.3 6.9 - - + +
326A SER 4.1 2.2 - - - +
327A ASN* 1.3 79.5 - - - +
329A VAL* 1.4 63.0 + - - +
330A ASN* 3.3 12.6 + - - +
331A VAL* 3.1 30.0 + - + +
332A LEU 3.0 17.5 + - - -
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Residues in contact with VAL 329 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
306A TYR* 4.9 4.7 - - - +
327A ASN* 4.1 2.2 - - - +
328A ASN* 1.4 73.5 - - - +
330A ASN* 1.3 71.7 + - - +
332A LEU* 3.6 15.4 - - + +
333A ASN* 2.9 37.2 + - - +
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Residues in contact with ASN 330 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21A GLN* 3.5 33.9 + - + +
328A ASN* 3.2 9.7 + - - +
329A VAL* 1.3 86.0 - - - +
331A VAL* 1.3 59.2 + - - +
333A ASN* 3.4 5.9 + - - +
334A THR* 2.9 32.2 + - - -
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Residues in contact with VAL 331 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18A ALA* 3.7 24.9 - - + +
21A GLN* 3.8 13.2 - - + -
23A ALA* 3.8 13.9 - - + +
306A TYR* 4.1 5.2 - - + -
323A ALA* 3.8 29.6 - - + -
325A THR* 4.0 13.5 - - + -
328A ASN* 3.1 33.6 + - - +
330A ASN* 1.3 77.5 - - - +
332A LEU* 1.3 61.6 + - - +
334A THR* 3.2 2.0 + - - -
335A MET* 2.9 29.2 + - + +
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Residues in contact with LEU 332 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
299A THR* 6.0 0.7 - - + -
300A GLY 5.4 1.1 - - - +
301A THR* 4.5 4.9 - - + -
306A TYR* 3.6 52.9 - - + +
307A THR 5.8 0.7 - - - +
308A TYR* 2.7 47.5 + - + +
328A ASN 3.0 7.2 + - - +
329A VAL* 3.2 18.4 + - + +
331A VAL* 1.3 77.9 - - - +
333A ASN* 1.3 63.8 + - - +
335A MET* 3.4 2.3 + - - -
336A ALA 3.4 6.9 + - - -
400A BSA 3.3 47.8 - - + -
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Residues in contact with ASN 333 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
308A TYR* 4.6 1.7 + - - -
329A VAL* 2.9 29.7 + - - +
330A ASN* 3.8 6.6 - - - +
332A LEU* 1.3 81.0 - - - +
334A THR* 1.3 67.4 + - - +
336A ALA* 3.3 18.6 + - - +
337A ARG* 3.8 7.1 + - - +
400A BSA 4.9 8.9 - - - -
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Residues in contact with THR 334 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14A VAL* 3.3 32.6 - - + +
17A THR* 3.8 14.0 - - + +
18A ALA* 3.7 17.0 - - + +
21A GLN* 2.6 29.9 + - - -
330A ASN 2.9 9.2 + - - -
331A VAL* 3.7 4.0 - - - -
333A ASN* 1.3 78.6 - - - +
335A MET* 1.3 58.6 + - - +
337A ARG* 2.9 43.6 + - - +
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Residues in contact with MET 335 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14A VAL* 4.3 7.0 - - - -
15A LEU* 4.1 16.8 - - + -
18A ALA* 3.7 24.9 - - + -
26A ALA* 4.1 8.1 - - + -
27A MET 4.1 4.9 - - - +
306A TYR* 5.4 4.3 - - + +
308A TYR* 3.7 24.5 - - + -
321A ALA* 3.8 27.4 - - + -
322A LEU 3.8 23.8 - - - +
323A ALA* 3.9 17.9 - - + +
331A VAL* 2.9 23.0 + - + +
332A LEU* 3.9 1.1 - - - +
333A ASN 3.3 0.4 - - - -
334A THR* 1.3 75.2 - - - +
336A ALA* 1.3 59.1 + - - +
338A THR* 2.8 31.9 + - + +
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Residues in contact with ALA 336 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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287A ARG* 3.6 24.5 + - - +
308A TYR* 3.4 30.9 - - + +
332A LEU 3.4 5.0 + - - +
333A ASN* 3.3 13.8 + - - +
334A THR 3.1 0.6 - - - -
335A MET* 1.3 76.6 - - - +
337A ARG* 1.3 62.3 + - - +
339A LEU* 3.1 23.9 + - - +
340A GLU* 4.1 3.5 + - - +
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Residues in contact with ARG 337 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10A GLY* 4.8 0.6 + - - -
13A ALA* 4.2 11.7 - - - +
14A VAL* 3.6 35.1 - - + +
17A THR* 3.5 36.2 + - - +
333A ASN 4.2 6.5 - - - +
334A THR* 2.9 28.0 + - - +
336A ALA* 1.3 75.1 - - - +
338A THR* 1.3 63.3 + - - +
339A LEU 3.1 0.2 - - - -
340A GLU* 3.1 16.7 + - + +
341A SER* 3.1 23.0 + - - -
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Residues in contact with THR 338 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11A LEU* 3.6 23.4 - - + +
14A VAL* 3.7 22.2 - - + +
15A LEU* 4.6 3.4 - - + -
28A VAL* 4.2 12.8 - - + -
308A TYR* 4.8 0.9 - - - +
319A VAL* 4.7 1.2 - - - +
321A ALA* 3.5 28.9 - - + +
335A MET* 2.8 30.5 + - + +
337A ARG* 1.3 79.4 - - - +
339A LEU* 1.3 67.4 + - - +
342A ALA* 2.9 32.6 + - - +
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Residues in contact with LEU 339 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
287A ARG* 3.6 35.7 - - - +
289A LEU* 3.7 16.9 - - + +
295A VAL* 4.4 7.0 - - + -
308A TYR* 4.2 15.7 - - + -
310A PHE* 3.8 36.3 - - + -
319A VAL* 4.3 15.0 - - + +
336A ALA 3.1 13.3 + - - +
338A THR* 1.3 82.0 + - - +
340A GLU* 1.3 66.1 + - + +
342A ALA* 4.7 0.4 - - - -
343A PHE* 2.9 46.0 + - + +
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Residues in contact with GLU 340 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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289A LEU* 3.5 16.7 - - + +
290A SER* 2.6 51.5 + - - -
336A ALA 4.9 2.2 - - - +
337A ARG* 3.1 19.8 + - + +
339A LEU* 1.3 76.7 - - - +
341A SER* 1.3 59.1 + - - +
344A CYS* 2.8 43.9 + - - +
345A GLY 3.2 3.1 + - - +
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Residues in contact with SER 341 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7A ASP* 3.0 36.1 + - - -
10A GLY* 3.5 20.1 + - - -
11A LEU* 3.8 31.0 - - - -
14A VAL* 4.2 4.2 - - - +
337A ARG 3.1 11.7 + - - -
338A THR* 4.8 0.2 - - - -
340A GLU* 1.3 77.7 - - - +
342A ALA* 1.3 61.1 + - - +
345A GLY* 3.4 14.9 + - - +
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Residues in contact with ALA 342 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6A PRO* 3.6 16.5 - - - +
7A ASP 4.7 0.2 - - - +
11A LEU* 4.4 6.3 - - + -
30A VAL* 3.8 16.2 - - + -
317A ARG* 2.8 32.4 + - - -
319A VAL* 3.4 32.5 - - + -
338A THR 2.9 18.7 + - - +
339A LEU 4.2 1.8 - - - +
341A SER* 1.3 80.3 - - - +
343A PHE* 1.3 51.9 + - + +
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Residues in contact with PHE 343 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3A LEU* 4.5 10.6 - - + +
4A PRO* 3.4 22.2 - - - +
289A LEU* 3.6 15.7 - - + -
293A ILE* 3.5 14.5 - - + +
295A VAL* 3.7 32.8 - - + -
310A PHE 3.6 21.5 - - - -
311A ALA* 4.1 0.2 - - - -
312A SER* 3.8 10.3 - - - -
317A ARG* 3.6 47.5 + - + +
319A VAL* 3.4 28.5 - - + -
339A LEU* 2.9 37.6 + - + +
342A ALA* 1.3 77.5 - - - +
344A CYS* 1.3 63.6 + - - +
345A GLY 3.4 0.2 - - - -
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Residues in contact with CYS 344 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4A PRO* 3.3 18.9 - - - +
289A LEU* 3.7 18.8 - - - -
290A SER* 4.7 0.9 - - - +
291A CYS* 2.1 56.1 - - + +
340A GLU* 2.8 39.0 + - + +
343A PHE* 1.3 74.1 - - - +
345A GLY* 1.3 65.3 + - - +
346A LYS 4.2 5.0 - - - +
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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
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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