Contacts of the helix formed by residues 292 - 310 (chain A) in PDB entry 4YD1
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 292 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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291A LEU* 1.3 75.1 - - - +
293A SER* 1.3 57.6 + - - +
295A VAL* 3.2 19.4 + - - +
296A ASP* 2.4 66.7 + - - +
299A GLN* 5.6 1.6 + - - -
317A LEU* 3.5 26.7 - - - +
321A PHE* 3.7 27.9 + - - +
325A LYS 4.0 8.7 - - - +
326A LEU* 3.7 29.1 + - + +
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Residues in contact with SER 293 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
291A LEU* 4.0 14.1 - - - +
292A ARG* 1.3 78.7 - - - +
294A ASP* 1.3 70.0 + - - +
296A ASP* 3.4 10.2 + - - +
297A ALA* 3.1 23.2 + - - +
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Residues in contact with ASP 294 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
290A VAL* 3.8 14.1 - - + -
291A LEU* 2.9 33.0 + - - +
293A SER* 1.3 78.6 + - - +
295A VAL* 1.3 61.8 + - - +
297A ALA* 3.3 3.8 + - - +
298A LEU* 2.9 38.6 + - + +
394A LEU* 3.5 24.0 - - + +
396A GLN* 3.9 10.0 + - - +
413A LYS* 2.8 36.8 + - - -
415A VAL* 5.2 0.7 - - + -
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Residues in contact with VAL 295 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
290A VAL* 4.3 0.4 - - + -
291A LEU 3.0 12.3 + - - +
292A ARG* 3.2 21.1 + - - +
294A ASP* 1.3 76.4 - - - +
296A ASP* 1.3 53.2 + - - +
298A LEU* 3.2 1.9 + - - +
299A GLN* 2.8 39.1 + - - +
317A LEU* 3.9 38.1 - - + -
321A PHE* 3.5 43.1 - - + -
331A VAL* 3.9 19.7 - - + -
333A PHE* 4.4 1.0 - - + -
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Residues in contact with ASP 296 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
292A ARG* 2.4 54.3 + - - +
293A SER* 3.8 7.8 - - - +
294A ASP 3.3 0.2 - - - -
295A VAL* 1.3 75.7 - - - +
297A ALA* 1.3 63.3 + - - +
299A GLN* 3.4 7.3 + - - +
300A GLN* 3.2 22.5 + - - +
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Residues in contact with ALA 297 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
293A SER 3.1 17.2 + - - +
294A ASP* 3.7 4.3 - - - +
296A ASP* 1.3 78.7 - - - +
298A LEU* 1.3 61.2 + - - +
300A GLN* 3.3 7.7 + - - +
301A VAL* 3.2 26.5 + - + +
394A LEU* 4.0 20.0 - - + -
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Residues in contact with LEU 298 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
294A ASP* 2.9 25.0 + - + +
295A VAL* 3.8 3.4 - - - +
297A ALA* 1.3 73.5 - - - +
299A GLN* 1.3 66.9 + - - +
301A VAL* 3.2 7.9 + - + +
302A VAL* 2.9 28.3 + - + +
331A VAL* 3.9 15.3 - - + -
333A PHE* 4.1 13.9 - - + -
392A PHE* 3.6 40.8 - - + -
393A ARG 5.7 0.2 - - - +
394A LEU* 3.9 23.8 - - + -
415A VAL* 3.7 35.4 - - + -
417A VAL* 4.2 6.1 - - + -
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Residues in contact with GLN 299 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
292A ARG* 5.6 1.9 + - - -
295A VAL* 2.8 20.5 + - - +
296A ASP* 3.7 7.6 - - - +
298A LEU* 1.3 77.6 - - - +
300A GLN* 1.3 55.2 + - - +
302A VAL* 4.0 0.6 - - - +
303A GLU* 2.8 65.1 + - + +
315A VAL* 3.9 17.6 + - + +
317A LEU* 3.8 30.6 - - - +
333A PHE* 3.5 24.4 - - + -
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Residues in contact with GLN 300 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
296A ASP 3.2 13.3 + - - +
297A ALA* 3.6 9.4 - - - +
298A LEU 3.3 0.2 - - - -
299A GLN* 1.3 79.3 - - - +
301A VAL* 1.3 58.4 + - + +
303A GLU* 3.8 10.9 - - - +
304A GLU* 2.9 30.4 + - + +
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Residues in contact with VAL 301 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
297A ALA* 3.2 14.2 + - + +
298A LEU* 3.2 13.4 + - + +
300A GLN* 1.3 79.4 - - + +
302A VAL* 1.3 58.2 + - - +
304A GLU* 3.3 7.0 + - - +
305A ALA* 3.0 27.7 + - - +
354A LEU* 3.6 14.5 - - + +
357A GLN* 5.1 2.9 - - - +
359A LEU* 3.6 33.2 - - + -
392A PHE* 4.0 15.5 - - + -
394A LEU* 5.8 3.8 - - + -
395A PRO* 6.2 2.9 - - + -
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Residues in contact with VAL 302 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
298A LEU* 2.9 20.2 + - + +
299A GLN* 4.0 3.1 - - - +
301A VAL* 1.3 73.0 - - - +
303A GLU* 1.3 61.2 + - - +
305A ALA* 3.2 5.1 + - - -
306A VAL* 2.8 50.2 + - + +
315A VAL* 4.1 18.2 - - + -
333A PHE* 3.9 21.8 - - + -
335A ILE* 4.8 1.1 - - + -
350A VAL* 5.6 1.3 - - + -
354A LEU* 5.0 3.4 - - + -
392A PHE* 4.0 29.4 - - + -
417A VAL* 4.6 0.9 - - + -
419A LEU* 4.0 23.1 - - + -
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Residues in contact with GLU 303 (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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299A GLN* 2.8 54.2 + - + +
300A GLN* 3.8 9.5 - - - +
302A VAL* 1.3 73.4 - - - +
304A GLU* 1.3 56.4 + - - +
306A VAL* 4.0 0.3 - - - +
307A GLY* 2.9 27.7 + - - -
315A VAL* 3.8 31.2 - - + +
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Residues in contact with GLU 304 (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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300A GLN* 2.9 21.4 + - + +
301A VAL* 3.6 7.0 - - - +
303A GLU* 1.3 76.2 - - - +
305A ALA* 1.3 59.4 + - - +
307A GLY 3.8 0.7 - - - -
308A GLN* 2.9 53.4 + - + +
357A GLN* 5.2 10.1 - - - +
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Residues in contact with ALA 305 (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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301A VAL 3.0 9.6 + - - +
302A VAL* 3.2 3.3 + - - +
304A GLU* 1.3 73.7 - - - +
306A VAL* 1.3 66.2 + - - +
308A GLN* 3.2 14.2 + - - +
309A ALA* 3.0 23.6 + - - +
350A VAL* 4.3 14.4 - - + +
353A ARG* 4.3 8.9 - - + -
354A LEU* 3.6 39.3 - - + +
357A GLN* 5.0 4.3 - - - +
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Residues in contact with VAL 306 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
302A VAL* 2.8 30.4 + - + +
303A GLU 4.0 1.1 - - - +
305A ALA* 1.3 72.7 - - - +
307A GLY* 1.3 56.8 + - - +
309A ALA* 3.1 1.9 + - - +
310A LEU* 3.0 28.8 + - - +
313A ALA* 3.5 31.2 - - + +
315A VAL* 3.7 24.2 - - + -
335A ILE* 3.7 36.6 - - + -
346A LEU* 4.7 3.8 - - + -
350A VAL* 4.0 20.4 - - + -
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Residues in contact with GLY 307 (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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303A GLU 2.9 17.8 + - - -
304A GLU* 3.8 1.6 - - - -
306A VAL* 1.3 77.8 - - - +
308A GLN* 1.3 61.8 + - - +
310A LEU 3.9 16.6 + - - -
311A PRO* 4.1 8.2 - - - +
312A GLY 5.8 0.7 - - - -
313A ALA 5.4 4.3 - - - -
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Residues in contact with GLN 308 (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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304A GLU* 2.9 37.4 + - + +
305A ALA* 3.5 12.5 - - - +
306A VAL 3.2 0.2 - - - -
307A GLY* 1.3 78.4 - - - +
309A ALA* 1.3 58.8 + - - +
310A LEU 3.5 0.2 - - - -
311A PRO* 5.2 2.9 - - - +
349A ARG* 4.1 5.4 + - - -
353A ARG* 3.9 33.2 + - - +
357A GLN* 4.9 14.1 + - - +
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Residues in contact with ALA 309 (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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305A ALA 3.0 16.4 + - - +
306A VAL 3.1 2.2 + - - +
308A GLN* 1.3 78.4 - - - +
310A LEU* 1.3 64.9 + - - +
311A PRO* 4.4 1.9 - - - +
346A LEU* 3.7 8.2 - - + +
349A ARG* 2.9 50.8 + - + +
350A VAL* 3.6 27.4 - - + +
353A ARG* 4.0 5.6 - - - +
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Residues in contact with LEU 310 (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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306A VAL 3.0 9.0 + - - +
307A GLY* 4.0 5.4 - - - +
308A GLN 3.5 0.8 - - - -
309A ALA* 1.3 82.8 - - - +
311A PRO* 1.3 81.6 - - + +
312A GLY 3.2 0.2 + - - -
313A ALA* 3.1 29.3 + - + +
337A HIS* 3.7 28.3 - - + +
342A GLN* 3.3 40.8 - - + +
343A GLU* 4.0 10.1 - - + -
346A LEU* 3.6 23.6 - - + -
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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