Contacts of the helix formed by residues 299 - 320 (chain A) in PDB entry 4NZP
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 ASP 299 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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297A THR 4.0 0.4 + - - -
298A LEU* 1.3 75.5 - - - +
300A ARG* 1.3 67.2 + - - +
301A GLU* 2.9 31.9 + - - +
302A ALA* 3.2 20.1 + - + +
303A ALA* 3.0 20.3 + - - +
366A LEU* 3.8 15.4 - - + +
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Residues in contact with ARG 300 (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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298A LEU 3.5 2.9 + - - -
299A ASP* 1.3 75.2 - - - +
301A GLU* 1.3 91.2 + - - +
303A ALA* 3.2 5.7 + - - +
304A HIS* 2.9 59.8 + - + +
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Residues in contact with GLU 301 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
299A ASP* 2.9 10.7 + - - +
300A ARG* 1.3 114.7 + - + +
302A ALA* 1.3 59.8 + - - +
304A HIS* 3.8 13.0 + - - +
305A LEU* 2.9 30.5 + - - +
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Residues in contact with ALA 302 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
298A LEU* 4.6 10.8 - - + -
299A ASP* 3.2 27.5 + - + +
300A ARG 3.2 0.8 - - - -
301A GLU* 1.3 75.4 - - - +
303A ALA* 1.3 64.3 + - - +
305A LEU* 3.5 7.2 + - - +
306A LYS* 3.2 22.7 + - - +
337A SER* 4.7 15.5 - - - -
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Residues in contact with ALA 303 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
291A ARG* 6.3 0.2 - - - +
294A GLU* 5.6 7.2 - - + +
298A LEU* 4.0 25.0 - - + +
299A ASP 3.0 12.9 + - - +
300A ARG* 3.5 9.6 - - - +
302A ALA* 1.3 78.3 - - - +
304A HIS* 1.3 64.7 + - + +
306A LYS* 3.4 7.8 + - - +
307A ASP* 3.0 33.9 + - - +
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Residues in contact with HIS 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 ARG* 2.9 45.1 + - + +
301A GLU* 4.1 16.6 + - - +
303A ALA* 1.3 82.2 - - + +
305A LEU* 1.3 65.3 + - - +
307A ASP* 3.3 15.3 + - - +
308A GLU* 3.1 36.4 + - - +
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Residues in contact with LEU 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 GLU 2.9 19.3 + - - +
302A ALA* 3.8 7.0 - - - +
303A ALA 3.3 0.2 - - - -
304A HIS* 1.3 78.9 - - - +
306A LYS* 1.3 62.1 + - - +
308A GLU* 3.2 25.0 + - + +
309A LEU* 3.3 28.1 + - + +
333A LEU* 4.2 24.9 - - + -
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Residues in contact with LYS 306 (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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82A ARG 2.8 21.9 + - - +
83A ALA* 3.9 11.3 + - + +
84A ASN* 3.2 19.0 - - - +
294A GLU* 2.6 32.5 + - - -
298A LEU* 4.3 5.8 - - - -
302A ALA 3.2 12.8 + - - +
303A ALA* 3.7 4.4 + - - +
305A LEU* 1.3 80.5 - - - +
307A ASP* 1.3 64.5 + - - +
309A LEU* 3.2 4.5 + - - +
310A MET* 3.0 22.2 + - - +
333A LEU* 4.6 12.6 - - + -
334A ILE* 4.1 29.4 - - + -
337A SER* 3.4 28.9 - - - +
338A GLN* 3.6 1.1 - - - +
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Residues in contact with ASP 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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83A ALA 5.4 1.6 - - - +
84A ASN* 4.5 3.3 + - - -
291A ARG* 2.7 38.2 + - - +
303A ALA* 3.0 22.1 + - - +
304A HIS* 3.5 20.7 - - - +
305A LEU 3.3 0.2 - - - -
306A LYS* 1.3 79.0 + - - +
308A GLU* 1.3 60.7 + - + +
310A MET* 3.3 17.1 + - - +
311A PRO* 3.5 11.8 - - - +
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Residues in contact with GLU 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 HIS* 3.1 25.6 + - + +
305A LEU* 3.2 19.3 + - + +
307A ASP* 1.3 78.0 - - + +
309A LEU* 1.3 65.8 + - + +
310A MET 3.7 0.3 + - - -
311A PRO* 3.9 8.5 - - - +
312A LYS* 5.4 1.2 + - - +
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Residues in contact with LEU 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 LEU* 3.3 25.0 + - + +
306A LYS* 3.2 7.4 + - - +
308A GLU* 1.3 82.5 - - + +
310A MET* 1.3 64.3 + - - +
311A PRO* 3.6 0.9 - - - -
312A LYS* 3.7 26.7 + - + +
313A TYR* 3.3 20.3 + - - +
330A LEU* 4.2 26.0 - - + +
333A LEU* 3.7 37.0 - - + -
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Residues in contact with MET 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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83A ALA* 3.4 27.4 - - + +
84A ASN* 3.7 5.4 - - + +
85A ALA* 3.7 12.1 - - - -
86A ILE* 3.3 49.8 - - + +
291A ARG* 4.8 12.6 - - - +
306A LYS 3.0 14.2 + - - +
307A ASP* 3.3 10.7 + - - +
309A LEU* 1.3 76.9 - - - +
311A PRO* 1.3 78.5 - - + +
313A TYR* 2.9 10.1 + - + +
314A ALA* 2.8 25.7 + - - -
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Residues in contact with PRO 311 (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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86A ILE 5.0 1.3 - - - +
87A TYR* 5.7 0.2 - - - -
307A ASP 3.5 11.0 - - - +
308A GLU 3.9 7.6 - - - +
309A LEU 3.8 1.6 - - - -
310A MET* 1.3 111.2 - - + +
312A LYS* 1.3 58.1 + - - +
314A ALA* 3.0 6.3 + - + +
315A SER* 2.8 32.8 + - - -
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Residues in contact with LYS 312 (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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308A GLU 5.4 1.1 + - - +
309A LEU* 3.7 29.1 + - + +
310A MET 3.3 0.6 - - - -
311A PRO* 1.3 76.8 - - - +
313A TYR* 1.3 58.3 + - - +
315A SER* 3.4 6.9 + - - +
316A LEU* 3.1 35.3 + - + +
330A LEU* 4.2 21.3 - - + -
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Residues in contact with TYR 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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79A PRO 3.6 0.2 + - - -
80A MET* 3.5 19.0 - - - -
83A ALA* 3.6 27.4 - - + -
85A ALA* 4.0 9.6 - - + -
309A LEU 3.3 10.6 + - - +
310A MET* 2.9 11.3 + - - +
312A LYS* 1.3 77.2 - - - +
314A ALA* 1.3 64.4 + - - +
316A LEU* 3.4 5.0 + - - +
317A ILE* 3.2 47.7 + - + +
322A TRP* 3.5 12.2 - + - -
327A ARG* 3.6 24.2 - - + -
330A LEU* 4.0 24.7 - - + +
331A GLN* 2.5 33.4 + - - -
334A ILE* 3.5 22.7 - - + -
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Residues in contact with ALA 314 (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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85A ALA* 4.6 1.1 - - + -
86A ILE 3.6 34.5 - - - +
87A TYR* 4.2 11.2 - - + -
93A LEU* 3.6 18.4 - - + +
310A MET* 2.8 15.5 + - - +
311A PRO* 3.4 10.1 - - + +
313A TYR* 1.3 76.4 - - - +
315A SER* 1.3 57.0 + - - +
317A ILE* 3.3 4.7 + - - +
318A TYR* 2.9 29.5 + - - +
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Residues in contact with SER 315 (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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87A TYR* 3.7 18.8 - - - -
311A PRO 2.8 16.5 + - - -
312A LYS* 3.8 7.0 - - - -
314A ALA* 1.3 72.3 - - - +
316A LEU* 1.3 61.2 + - - +
318A TYR* 4.2 6.3 - - - -
319A ASN* 2.8 49.7 + - - +
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Residues in contact with LEU 316 (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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312A LYS* 3.1 21.0 + - + +
313A TYR* 3.5 8.3 - - - +
315A SER* 1.3 75.4 - - - +
317A ILE* 1.3 57.7 + - - +
319A ASN* 3.6 0.8 + - - +
320A GLY 3.3 3.1 + - - -
321A TYR* 2.7 67.1 + - + +
324A SER* 4.7 0.2 - - - +
326A GLU* 3.8 35.7 - - + +
327A ARG* 4.2 14.4 - - + +
330A LEU* 3.6 31.0 - - + -
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Residues in contact with ILE 317 (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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80A MET* 3.6 28.0 - - + -
93A LEU* 4.2 15.3 - - + -
96A SER* 3.5 33.7 - - - +
97A ILE* 4.3 9.2 - - + +
131A ARG* 4.7 0.3 + - - -
313A TYR* 3.2 49.9 + - + +
314A ALA 3.6 6.3 - - - +
315A SER 3.2 0.6 - - - -
316A LEU* 1.3 73.3 - - - +
318A TYR* 1.3 69.2 + - - +
320A GLY* 3.1 13.9 + - - -
321A TYR 4.3 0.8 + - - +
322A TRP* 3.8 29.3 + - + +
327A ARG* 4.9 2.7 - - + -
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Residues in contact with TYR 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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87A TYR* 3.8 34.3 - + + -
91A TYR* 3.8 18.2 - + - -
93A LEU* 3.8 5.3 - - + +
96A SER* 3.6 19.3 - - - -
127A ASN* 2.9 32.4 + - - +
131A ARG* 3.0 41.2 + - - -
266A GLU* 2.7 31.7 + - - +
267A ASN 3.4 25.8 + - - -
268A ARG* 3.4 4.3 - - - +
269A TYR* 3.7 10.5 - - - +
314A ALA 2.9 17.5 + - - +
315A SER 3.7 3.8 - - - +
317A ILE* 1.3 78.7 - - - +
319A ASN* 1.3 70.3 + - - +
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Residues in contact with ASN 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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87A TYR* 4.9 2.6 + - - -
127A ASN 5.4 0.2 - - - +
130A VAL* 3.5 24.4 - - - +
131A ARG* 4.5 2.4 - - - +
269A TYR* 3.3 48.6 - - + +
315A SER* 2.8 38.2 + - - +
316A LEU* 5.0 0.8 - - - +
318A TYR* 1.3 90.5 - - - +
320A GLY* 1.3 58.9 + - - +
321A TYR* 3.6 20.8 - - + -
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Residues in contact with GLY 320 (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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96A SER 5.9 0.7 - - - -
100A PRO* 6.5 0.9 - - - -
131A ARG* 4.0 27.6 - - - +
134A LEU* 3.4 26.3 - - - +
135A GLY 5.0 0.5 + - - -
317A ILE 3.1 11.4 + - - -
318A TYR 3.2 1.0 + - - -
319A ASN* 1.3 80.8 - - - +
321A TYR* 1.3 62.0 + - - +
322A TRP* 3.4 5.4 + - - -
323A PHE 5.0 1.0 + - - -
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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
------------------------------------------------------------
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