Contacts of the helix formed by residues 303 - 324 (chain A) in PDB entry 2NZ2
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 303 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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302A MET* 1.3 78.3 - - - +
304A ARG* 1.3 68.7 + - - +
305A GLU* 2.7 31.7 + - - +
306A VAL* 2.9 26.7 + - + +
307A ARG* 3.0 22.2 + - - +
369A LEU* 3.3 15.4 - - + +
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Residues in contact with ARG 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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302A MET 3.6 2.7 + - - -
303A ASP* 1.3 79.1 + - - +
305A GLU* 1.3 92.2 + - + +
307A ARG* 3.4 14.5 - - - +
308A LYS* 3.4 28.1 - - + +
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Residues in contact with GLU 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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303A ASP* 2.7 14.5 + - - +
304A ARG* 1.3 110.9 + - + +
306A VAL* 1.3 69.4 + - - +
307A ARG 3.1 0.8 + - - -
308A LYS* 2.8 41.9 + - - +
309A ILE* 3.5 23.7 + - + +
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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 MET* 4.2 18.6 - - + -
303A ASP* 2.9 32.3 + - + +
305A GLU* 1.3 78.6 - - - +
307A ARG* 1.3 56.1 + - - +
309A ILE* 3.3 8.7 + - + +
310A LYS* 2.8 29.8 + - + +
341A SER* 4.5 19.7 - - - +
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Residues in contact with ARG 307 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
295A LEU* 3.9 26.3 + - - +
298A GLU* 4.0 11.8 + - - +
299A ALA* 4.5 24.0 - - - +
302A MET* 3.8 24.7 - - + -
303A ASP 3.0 13.7 + - - +
304A ARG* 3.4 15.0 - - - +
305A GLU 3.1 0.4 - - - -
306A VAL* 1.3 77.8 - - - +
308A LYS* 1.3 60.2 + - + +
310A LYS* 3.4 1.9 + - + +
311A GLN* 2.8 68.7 + - + +
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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
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304A ARG* 3.4 30.1 - - + +
305A GLU* 2.8 45.9 + - - +
306A VAL 3.4 0.4 - - - -
307A ARG* 1.3 76.2 - - + +
309A ILE* 1.3 65.7 + - + +
311A GLN* 3.7 6.5 + - - +
312A GLY* 3.4 16.5 + - - -
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Residues in contact with ILE 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 GLU* 3.5 21.5 + - + +
306A VAL* 3.3 9.4 + - + +
308A LYS* 1.3 77.8 - - + +
310A LYS* 1.3 64.1 + - - +
312A GLY* 3.3 10.4 + - - -
313A LEU* 3.3 25.0 + - + +
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Residues in contact with LYS 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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78A GLN 2.6 30.7 + - - -
79A SER* 3.0 20.0 + - - +
80A SER* 2.8 20.4 + - - -
298A GLU* 3.0 13.8 + - - +
302A MET* 4.5 6.3 - - - -
306A VAL* 2.8 20.5 + - + +
307A ARG* 3.6 7.0 - - - +
309A ILE* 1.3 78.4 - - - +
311A GLN* 1.3 67.8 + - + +
313A LEU* 3.1 15.5 + - + +
314A GLY 3.0 23.4 + - - -
338A ILE* 4.4 13.0 - - + -
341A SER* 3.2 31.4 - - - +
342A GLN* 3.8 6.7 - - - +
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Residues in contact with GLN 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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79A SER 3.3 11.1 + - - -
80A SER* 3.4 22.6 + - - +
81A ALA* 5.3 1.9 - - - +
295A LEU* 4.5 2.1 - - - +
298A GLU* 3.9 5.8 + - - -
307A ARG* 2.8 57.5 + - + +
308A LYS* 4.1 6.3 - - - +
309A ILE 3.3 0.4 - - - -
310A LYS* 1.3 106.4 - - + +
312A GLY* 1.3 61.5 + - - +
314A GLY* 3.8 1.0 - - - +
315A LEU* 3.1 32.5 + - - +
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Residues in contact with GLY 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 LYS 3.4 9.4 + - - -
309A ILE 3.3 7.0 + - - -
310A LYS 3.2 0.8 - - - -
311A GLN* 1.3 77.4 - - - +
313A LEU* 1.3 63.4 + - - +
315A LEU* 3.4 11.6 + - - +
316A LYS* 3.1 20.8 + - - +
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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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309A ILE* 3.3 26.8 + - + +
310A LYS* 3.1 16.6 + - + +
312A GLY* 1.3 75.2 - - - +
314A GLY* 1.3 53.3 + - - +
316A LYS* 3.0 10.1 + - + +
317A PHE 2.7 30.0 + - - -
333A PHE* 5.6 5.6 - - + -
334A VAL* 3.5 23.3 - - + +
337A CYS* 3.5 40.2 - - + +
338A ILE* 4.0 14.6 - - + +
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Residues in contact with GLY 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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79A SER* 3.6 23.8 - - - -
81A ALA* 3.5 12.8 - - - +
310A LYS 3.0 12.3 + - - -
311A GLN 4.0 1.6 - - - -
312A GLY 3.4 0.2 - - - -
313A LEU* 1.3 71.3 - - - +
315A LEU* 1.3 53.4 + - - +
317A PHE* 3.0 5.7 + - - +
318A ALA 2.8 31.5 + - - -
338A ILE* 3.9 14.7 - - - +
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Residues in contact with LEU 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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81A ALA* 3.9 11.5 - - + +
82A LEU 4.5 16.4 - - - +
84A GLU 6.1 0.2 - - - +
85A ASP* 5.5 7.0 - - - +
311A GLN 3.1 16.9 + - - +
312A GLY* 3.5 13.9 - - - +
313A LEU 3.3 0.2 - - - -
314A GLY* 1.3 75.2 - - - +
316A LYS* 1.3 62.4 + - - +
318A ALA* 3.4 5.2 + - + +
319A GLU* 3.3 20.1 + - - +
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Residues in contact with LYS 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 GLY 3.1 12.0 + - - +
313A LEU* 3.0 13.8 + - + +
315A LEU* 1.3 76.9 - - - +
317A PHE* 1.3 62.1 + - - +
319A GLU* 3.2 35.1 + - + +
320A LEU* 3.0 58.6 + - + +
330A GLU* 5.9 2.2 - - + -
334A VAL* 4.3 11.9 - - + -
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Residues in contact with PHE 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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75A PRO* 4.2 4.5 - - + -
76A ALA* 3.6 39.3 - - + -
79A SER* 3.6 19.3 - - - -
89A LEU* 4.5 9.4 - - + -
93A LEU* 4.3 1.8 - - + -
313A LEU 2.7 15.8 + - - +
314A GLY 3.2 7.2 - - - +
316A LYS* 1.3 71.9 - - - +
318A ALA* 1.3 67.2 + - - +
320A LEU* 3.3 6.2 + - - +
321A VAL* 3.0 55.4 + - + +
326A TRP* 3.7 20.2 - + - -
331A CYS* 4.0 5.2 - - - -
334A VAL* 3.7 14.8 - - + +
335A ARG* 3.7 32.5 - - + -
338A ILE* 3.7 11.9 - - + -
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Residues in contact with ALA 318 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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81A ALA* 4.2 15.3 - - + +
82A LEU 4.2 3.1 - - - +
83A TYR* 4.1 28.2 - - - +
89A LEU* 3.7 23.4 - - + +
314A GLY 2.8 17.9 + - - +
315A LEU* 3.7 7.0 - - + +
316A LYS 3.3 0.4 - - - -
317A PHE* 1.3 74.4 - - + +
319A GLU* 1.3 57.5 + - - +
321A VAL 3.7 0.2 + - - -
322A TYR* 3.0 29.8 + - - +
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Residues in contact with GLU 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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83A TYR* 4.4 23.1 - - + -
273A PHE* 5.9 0.9 - - - -
315A LEU 3.3 9.2 + - - +
316A LYS* 3.2 33.9 + - + +
318A ALA* 1.3 76.7 - - - +
320A LEU* 1.3 63.5 + - - +
322A TYR* 4.1 0.2 - - - +
323A THR* 2.8 50.8 + - + +
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Residues in contact with LEU 320 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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316A LYS* 3.0 52.5 + - + +
317A PHE* 3.3 5.1 + - - +
319A GLU* 1.3 77.1 - - - +
321A VAL* 1.3 61.7 + - - +
323A THR* 3.4 3.3 + - - +
324A GLY 3.2 3.6 + - - -
325A PHE* 2.7 47.4 + - + -
328A SER* 4.7 0.2 - - - +
330A GLU* 3.4 37.2 - - + +
331A CYS* 3.8 39.7 - - + +
334A VAL* 4.5 3.1 - - + -
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Residues in contact with VAL 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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89A LEU* 4.4 6.1 - - + -
92A SER* 3.2 33.4 + - - +
93A LEU* 3.7 22.9 - - + -
96A PRO* 5.8 0.7 - - + -
127A ARG* 3.9 6.1 + - - -
317A PHE* 3.0 51.8 + - + +
318A ALA 3.9 3.1 - - - +
320A LEU* 1.3 75.0 - - - +
322A TYR* 1.3 66.8 + - - +
324A GLY* 3.2 12.1 + - - -
325A PHE 4.8 1.1 - - - +
326A TRP* 4.0 20.2 - - + +
331A CYS* 4.4 4.5 - - - -
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Residues in contact with TYR 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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83A TYR* 3.3 44.9 - + + -
87A TYR* 3.7 22.2 - + - -
89A LEU* 3.9 3.1 - - + +
92A SER* 4.0 4.5 - - - -
123A ASN* 2.7 32.8 + - - +
127A ARG* 2.7 52.2 + - - +
270A GLU* 2.5 39.3 + - - +
271A ASN 3.2 22.6 + - - -
272A ARG* 3.5 5.0 - - - -
273A PHE* 4.1 2.7 - - - -
318A ALA 3.0 20.4 + - - +
319A GLU 4.1 1.3 - - - +
320A LEU 3.5 0.2 - - - -
321A VAL* 1.3 75.8 - - - +
323A THR* 1.3 66.5 + - + +
502A CIR 3.7 2.0 - - - -
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Residues in contact with THR 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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83A TYR* 5.4 2.2 - - + +
126A VAL* 3.3 25.7 - - - +
127A ARG* 4.4 2.0 - - - -
273A PHE* 3.4 49.7 - - + -
319A GLU* 2.8 40.2 + - + +
320A LEU* 3.4 4.2 + - - +
322A TYR* 1.3 85.8 - - + +
324A GLY* 1.3 58.6 + - - +
325A PHE* 3.1 22.1 - - - -
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Residues in contact with GLY 324 (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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127A ARG* 3.6 32.7 - - - +
130A LEU* 3.4 24.4 - - - +
131A SER* 4.7 5.0 + - - -
320A LEU 3.2 2.6 + - - -
321A VAL 3.2 8.2 + - - -
322A TYR 3.3 0.4 - - - -
323A THR* 1.3 79.9 - - - +
325A PHE* 1.3 62.6 + - - +
326A TRP 3.5 4.9 + - - -
327A HIS 5.0 0.9 + - - -
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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
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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