Contacts of the helix formed by residues 306 - 324 (chain A) in PDB entry 3N9Z
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 306 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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302A GLU* 2.7 40.1 + - - +
303A MET 3.3 6.3 - - - +
304A ALA 3.3 0.2 - - - -
305A ARG* 1.3 102.9 + - - +
307A LEU* 1.3 65.0 + - - +
308A LYS* 3.3 3.4 - - - -
309A VAL* 3.0 31.0 + - + +
310A GLN 3.0 9.7 + - - -
395A ASN* 4.3 11.8 - - - +
396A PHE* 3.6 21.2 + - + +
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Residues in contact with LEU 307 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303A MET 3.7 2.9 - - - +
304A ALA 3.6 21.8 - - - +
305A ARG 3.9 1.0 + - - -
306A ASN* 1.3 73.2 - - - +
308A LYS* 1.3 59.4 + - + +
310A GLN* 3.4 24.6 + - - +
311A ASP* 3.0 36.6 + - - +
446A VAL 3.9 10.1 - - - +
447A GLU* 4.5 19.7 - - + +
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Residues in contact with LYS 308 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
306A ASN 3.3 0.8 - - - -
307A LEU* 1.3 79.0 - - + +
309A VAL* 1.3 67.7 + - + +
311A ASP* 3.4 12.2 + - - +
312A MET* 3.1 30.0 + - - +
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Residues in contact with VAL 309 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
302A GLU 5.6 0.2 - - - +
303A MET* 5.7 0.9 - - + -
306A ASN* 3.0 21.5 + - + +
308A LYS* 1.3 75.7 - - + +
310A GLN* 1.3 67.2 + - - +
312A MET* 3.2 16.1 + - + +
313A LEU* 3.0 32.9 + - + +
337A LEU* 5.9 1.1 - - + -
396A PHE* 3.8 35.7 - - + +
397A ASP* 5.5 0.2 - - - -
398A PRO* 3.8 30.7 - - + -
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Residues in contact with GLN 310 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303A MET* 3.1 56.6 - - + +
306A ASN 3.0 6.3 + - - -
307A LEU* 3.6 15.3 - - - +
309A VAL* 1.3 76.3 - - - +
311A ASP* 1.3 56.4 + - - +
313A LEU* 3.2 4.0 + - - +
314A ARG* 2.8 64.6 + - - +
441A LEU* 4.1 1.6 - - + +
445A ARG* 3.5 4.4 - - - +
446A VAL* 2.9 47.6 + - - +
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Residues in contact with ASP 311 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
307A LEU* 3.0 23.6 + - - +
308A LYS* 3.5 15.8 - - - +
310A GLN* 1.3 75.9 - - - +
312A MET* 1.3 61.6 + - - +
314A ARG* 3.3 18.5 + - - +
315A ALA* 3.0 24.4 + - - +
445A ARG* 5.6 3.3 + - - -
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Residues in contact with MET 312 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
308A LYS* 3.1 19.6 + - - +
309A VAL* 3.2 19.5 + - + +
311A ASP* 1.3 76.2 - - - +
313A LEU* 1.3 60.5 + - - +
315A ALA* 3.4 6.4 + - - +
316A GLU* 3.1 23.6 + - - +
337A LEU* 3.7 28.7 - - + +
399A THR* 4.2 22.7 - - + -
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Residues in contact with LEU 313 (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 HIS* 4.1 4.0 - - - +
303A MET* 3.7 26.9 - - + -
309A VAL* 3.0 35.0 + - + +
310A GLN* 3.6 3.8 - - - +
312A MET* 1.3 74.9 - - - +
314A ARG* 1.3 65.1 + - - +
316A GLU* 3.4 4.6 + - - +
317A VAL* 3.1 27.5 + - - +
337A LEU* 3.6 42.2 - - + +
338A LEU* 3.7 19.5 - - + +
341A SER* 3.8 18.4 - - - +
396A PHE* 5.1 0.7 - - + -
398A PRO* 5.1 1.3 - - + -
441A LEU* 3.8 14.6 - - + -
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Residues in contact with ARG 314 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
310A GLN* 2.8 48.8 + - - +
311A ASP* 3.7 20.9 + - - +
313A LEU* 1.3 75.9 - - - +
315A ALA* 1.3 56.6 + - - +
317A VAL* 3.2 3.3 + - - +
318A LEU* 2.9 47.0 + - + +
441A LEU* 2.8 47.8 + - + +
444A PHE 2.5 28.1 + - - -
445A ARG* 3.4 17.9 - - - +
446A VAL* 5.2 0.2 - - - +
475A PHE* 3.6 34.1 - - + -
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Residues in contact with ALA 315 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
311A ASP 3.0 16.8 + - - +
312A MET* 3.8 6.7 - - - +
314A ARG* 1.3 75.5 - - - +
316A GLU* 1.3 58.0 + - - +
318A LEU* 3.9 9.9 - - - +
319A ALA* 3.0 30.1 + - - +
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Residues in contact with GLU 316 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
312A MET 3.1 16.9 + - - +
313A LEU* 3.8 6.2 - - - +
314A ARG 3.3 0.2 - - - -
315A ALA* 1.3 76.3 - - - +
317A VAL* 1.3 56.4 + - - +
319A ALA* 3.5 5.4 + - + +
320A ALA* 2.9 27.5 + - - +
334A LEU 4.0 9.4 - - - +
335A VAL* 3.3 19.9 - - - +
336A PRO* 3.1 15.1 - - - +
337A LEU* 2.9 35.0 + - + +
338A LEU* 3.2 25.1 + - - +
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Residues in contact with VAL 317 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
313A LEU 3.1 21.2 + - - +
314A ARG* 3.6 6.5 - - - +
316A GLU* 1.3 76.8 - - + +
318A LEU* 1.3 59.4 + - + +
320A ALA* 3.2 4.3 + - - -
321A ARG* 2.9 28.1 + - - +
331A MET* 3.6 4.3 - - + +
335A VAL* 4.3 8.3 - - + -
338A LEU* 4.1 22.7 - - + -
438A ILE* 3.9 26.2 - - + +
441A LEU* 4.0 22.0 - - + -
442A GLU* 3.8 28.0 - - + +
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Residues in contact with LEU 318 (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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314A ARG* 2.9 27.3 + - + +
315A ALA* 3.9 8.1 - - - +
317A VAL* 1.3 73.9 - - + +
319A ALA* 1.3 64.6 + - - +
321A ARG* 3.5 6.1 + - + +
322A HIS* 3.2 22.3 + - - +
442A GLU* 4.2 26.7 - - + +
475A PHE* 4.0 36.3 - - + -
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Residues in contact with ALA 319 (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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315A ALA 3.0 17.2 + - - +
316A GLU* 3.8 7.4 - - + +
318A LEU* 1.3 75.7 - - - +
320A ALA* 1.3 58.5 + - - +
322A HIS* 3.4 7.7 + - - +
323A GLN* 2.9 34.9 + - - +
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Residues in contact with ALA 320 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
316A GLU 2.9 18.8 + - - +
317A VAL 3.2 4.4 + - - +
319A ALA* 1.3 75.1 - - - +
321A ARG* 1.3 59.9 + - - +
323A GLN* 3.8 6.4 - - - +
324A ALA* 3.0 33.3 + - - +
331A MET* 3.7 9.5 - - + +
334A LEU* 3.6 32.1 - - + +
335A VAL* 3.7 15.9 - - + -
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Residues in contact with ARG 321 (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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133A ASP* 5.2 3.8 + - - -
317A VAL 2.9 12.2 + - - +
318A LEU* 4.0 6.5 - - + +
320A ALA* 1.3 76.2 - - - +
322A HIS* 1.3 62.6 + - - +
324A ALA 3.8 0.2 - - - -
325A GLN* 3.2 2.4 + - - -
326A GLY* 2.9 63.7 + - - -
328A MET* 3.7 20.0 - - - +
331A MET* 3.4 24.7 - - - +
438A ILE* 3.7 13.5 - - - +
439A ASN* 4.3 9.9 + - - -
442A GLU* 2.7 45.4 + - - +
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Residues in contact with HIS 322 (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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318A LEU 3.2 16.0 + - - +
319A ALA* 3.7 6.3 - - - +
321A ARG* 1.3 77.1 - - - +
323A GLN* 1.3 66.8 + - + +
325A GLN* 2.9 26.7 + - - +
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Residues in contact with GLN 323 (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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319A ALA* 2.9 25.2 + - - +
320A ALA* 3.8 4.3 - - - +
322A HIS* 1.3 80.5 - - + +
324A ALA* 1.3 58.3 + - - +
325A GLN* 3.5 5.7 + - - +
330A THR* 5.3 0.9 - - - +
334A LEU* 4.0 25.8 - - + +
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Residues in contact with ALA 324 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
320A ALA 3.0 19.1 + - - +
321A ARG 4.1 2.0 - - - +
323A GLN* 1.3 75.1 - - - +
325A GLN* 1.3 69.8 + - - +
326A GLY 3.2 0.2 + - - -
327A ASP* 3.3 37.6 + - - +
330A THR* 3.7 26.0 + - + +
331A MET* 3.7 13.0 - - + +
334A LEU* 4.1 1.3 - - + -
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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
------------------------------------------------------------
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