Contacts of the helix formed by residues 300 - 319 (chain A) in PDB entry 5IYB
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 ALA 300 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
299A ALA* 1.3 85.0 - - - +
301A HIS* 1.3 62.7 + - - +
302A VAL 3.2 1.9 - - - +
303A ILE* 3.1 12.5 + - - +
304A ALA* 2.9 27.0 + - - +
92Q TYR* 4.2 21.1 + - + +
94Q ILE* 5.1 15.7 - - + -
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Residues in contact with HIS 301 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
299A ALA* 3.8 16.0 - - + +
300A ALA* 1.3 76.7 + - - +
302A VAL* 1.3 84.7 + - + +
304A ALA* 3.2 8.0 + - - +
305A GLU* 2.9 29.1 + - - +
92Q TYR* 4.7 3.8 + - + -
28X C 5.8 2.7 + - - -
29X G 5.4 5.5 + - - -
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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
----------------------------------------------------------
293A ASN* 3.9 21.5 - - - +
299A ALA* 4.0 16.2 - - + +
300A ALA 3.2 0.2 - - - -
301A HIS* 1.3 105.0 - - + +
303A ILE* 1.3 59.2 + - - +
305A GLU* 3.5 8.9 - - + +
306A ASP* 2.9 34.1 + - - +
28X C 5.6 5.6 - - - +
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Residues in contact with ILE 303 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92A LYS* 3.7 29.8 - - - -
290A LEU* 3.5 24.7 - - + -
293A ASN* 4.7 7.6 - - - +
294A GLU* 4.9 7.6 - - + +
298A ALA* 3.4 39.9 - - + -
299A ALA 4.5 1.1 - - - +
300A ALA* 3.1 16.1 + - - +
302A VAL* 1.3 78.1 - - + +
304A ALA* 1.3 59.4 + - - +
306A ASP* 3.2 2.4 + - - +
307A VAL* 2.9 33.2 + - + +
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Residues in contact with ALA 304 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
300A ALA 2.9 12.4 + - - +
301A HIS* 3.2 11.9 + - - +
303A ILE* 1.3 76.3 - - - +
305A GLU* 1.3 58.3 + - - +
307A VAL* 3.5 6.9 + - - +
308A LYS* 3.0 28.2 + - - +
92Q TYR* 5.2 6.1 - - - +
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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
----------------------------------------------------------
301A HIS 2.9 17.7 + - - +
302A VAL* 3.5 11.7 - - + +
304A ALA* 1.3 74.7 - - - +
306A ASP* 1.3 62.7 + - - +
308A LYS* 3.2 7.5 + - - +
309A LEU* 2.8 31.4 + - + +
102M GLN* 3.2 38.2 + - - +
105M ARG* 3.2 28.1 + - - +
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Residues in contact with ASP 306 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
286A ILE* 4.6 9.1 - - - +
289A GLN* 4.7 4.0 - - - +
290A LEU* 3.4 53.3 + - + +
293A ASN* 3.7 12.6 + - - -
302A VAL* 2.9 23.6 + - - +
303A ILE 3.2 2.0 + - - +
305A GLU* 1.3 77.7 - - - +
307A VAL* 1.3 61.9 + - - +
309A LEU* 3.8 13.5 - - - +
310A LEU* 2.9 29.6 + - - +
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Residues in contact with VAL 307 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92A LYS* 3.9 33.4 - - + -
93A PRO 5.6 1.1 - - - +
94A VAL* 4.5 16.7 - - + +
218A PRO* 5.1 15.9 - - + -
290A LEU* 4.7 7.0 - - + -
303A ILE* 2.9 26.3 + - + +
304A ALA* 3.8 7.4 - - - +
306A ASP* 1.3 75.0 - - - +
308A LYS* 1.3 54.4 + - - +
310A LEU* 3.2 8.1 + - + +
311A GLN* 2.7 36.9 + - + +
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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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197A GLU* 2.3 39.8 + - - -
304A ALA 3.0 17.9 + - - +
305A GLU* 3.2 4.5 + - - +
307A VAL* 1.3 79.5 - - - +
309A LEU* 1.3 57.6 + - - +
311A GLN* 3.5 6.7 + - + +
312A PHE* 3.0 23.0 + - - +
325A LEU* 6.3 1.0 - - - +
93M PHE* 3.5 24.4 - - + +
101M TYR* 3.4 36.1 + - + -
102M GLN* 3.2 23.3 - - + +
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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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286A ILE* 3.7 32.8 - - + -
305A GLU* 2.8 21.5 + - + +
306A ASP* 3.9 13.0 - - - +
308A LYS* 1.3 71.3 - - - +
310A LEU* 1.3 59.0 + - - +
312A PHE* 3.3 2.8 + - - +
313A HIS* 3.0 50.8 + - + +
84M ILE* 4.6 11.2 - - + -
101M TYR* 3.6 10.1 - - - +
102M GLN* 3.5 20.6 + - - +
103M ASN 6.0 1.3 - - - +
105M ARG* 5.1 17.7 - - + +
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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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90A LEU* 4.4 13.9 - - + -
91A ALA 4.9 0.9 - - - +
92A LYS* 4.2 12.6 - - + +
94A VAL* 4.1 20.4 - - + -
283A ILE* 4.2 15.9 - - + +
286A ILE* 3.5 26.6 - - + +
287A ASN* 4.2 17.9 - - + +
290A LEU* 4.7 15.7 - - + -
306A ASP 2.9 20.2 + - - +
307A VAL* 3.5 5.2 - - + +
309A LEU* 1.3 74.1 - - - +
311A GLN* 1.3 64.1 + - - +
314A VAL* 3.1 43.8 + - + +
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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
----------------------------------------------------------
94A VAL* 3.6 11.1 - - + +
95A PHE* 2.8 66.1 + - - +
97A VAL 5.2 0.4 - - - +
196A LEU* 4.1 30.1 - - + +
197A GLU* 6.4 0.2 - - + -
218A PRO* 4.9 1.7 - - - +
307A VAL* 2.7 24.6 + - + +
308A LYS* 3.7 9.0 - - + +
310A LEU* 1.3 72.4 - - - +
312A PHE* 1.3 62.3 + - - +
314A VAL* 3.4 7.7 - - - +
315A ALA* 3.2 25.8 + - - +
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Residues in contact with PHE 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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196A LEU* 4.2 8.1 - - + -
279A LYS* 4.4 1.6 - - - -
308A LYS 3.0 9.8 + - - +
309A LEU 3.5 2.5 - - - +
310A LEU 3.2 0.2 - - - -
311A GLN* 1.3 75.0 - - - +
313A HIS* 1.3 71.4 + + - +
315A ALA* 3.3 1.7 + - - +
316A THR* 2.5 64.6 + - + +
325A LEU* 4.1 28.7 - - + -
326A PRO* 3.5 36.1 - - + -
327A ARG 4.8 0.7 - - - -
328A ALA* 4.5 6.1 - - + -
84M ILE* 4.4 25.1 - - + -
101M TYR* 3.0 43.5 - + + +
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Residues in contact with HIS 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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279A LYS* 3.0 28.3 + - - +
282A ASP* 3.1 44.3 + - + -
283A ILE* 3.5 18.9 - - + +
286A ILE* 3.8 21.3 - - + -
309A LEU* 3.0 39.7 + - + +
310A LEU 4.1 2.2 - - - +
312A PHE* 1.3 89.7 - + - +
314A VAL* 1.3 56.9 + - - +
316A THR* 3.0 4.8 + - - -
317A MET* 2.9 27.9 + - - +
84M ILE* 4.3 15.3 - - + -
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Residues in contact with VAL 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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90A LEU* 5.0 3.8 - - + -
94A VAL* 4.0 16.4 - - + -
95A PHE 4.4 4.3 - - - +
96A HIS* 6.1 1.1 - - + -
250A VAL* 5.1 3.4 - - + -
253A LEU* 4.3 22.4 - - + +
283A ILE* 3.7 24.0 - - + -
310A LEU* 3.1 37.8 + - + +
311A GLN* 3.4 21.5 - - - +
313A HIS* 1.3 76.0 - - - +
315A ALA* 1.3 67.1 + - - +
317A MET* 3.4 4.5 + - - +
318A VAL* 3.2 26.2 + - - +
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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
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96A HIS* 6.6 0.2 - - - -
97A VAL* 3.8 28.8 - - + +
196A LEU* 3.7 25.4 - - + -
311A GLN* 3.2 20.7 + - - +
312A PHE 3.7 0.7 - - - +
314A VAL* 1.3 82.7 - - - +
316A THR* 1.3 51.9 + - - +
318A VAL* 3.0 5.0 + - - +
319A ASP 2.5 37.9 + - - +
322A LEU* 4.3 3.4 - - + -
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Residues in contact with THR 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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279A LYS* 3.0 24.1 + - - -
312A PHE* 2.5 53.9 + - + +
313A HIS* 3.0 10.6 + - - -
315A ALA* 1.3 73.3 - - - +
317A MET* 1.3 59.5 + - - +
319A ASP 3.1 18.2 - - - +
320A ASN* 3.5 32.8 + - - +
322A LEU* 3.8 17.9 - - + -
326A PRO 4.9 1.3 - - - +
328A ALA* 4.1 2.0 - - + -
336A LEU* 5.1 3.8 - - - +
338A SER* 3.7 4.3 - - - -
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Residues in contact with MET 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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253A LEU* 4.9 10.5 - - + -
254A PRO 5.0 5.6 - - - +
256A PRO* 4.3 24.2 - - + -
276A LEU* 4.4 28.1 - - + +
279A LYS* 4.0 20.6 - - + +
280A LEU* 4.3 21.3 - - + -
283A ILE* 3.9 19.3 - - + -
313A HIS 2.9 19.3 + - - +
314A VAL* 3.5 6.7 - - - +
316A THR* 1.3 78.7 + - - +
318A VAL* 1.3 65.9 + - + +
336A LEU* 5.8 1.1 - - - -
338A SER* 4.0 1.8 - - - +
339A LEU* 3.2 31.6 + - + +
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Residues in contact with VAL 318 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96A HIS* 3.7 37.7 - - + +
97A VAL* 4.0 14.4 - - + -
98A GLY* 5.2 1.3 - - - +
253A LEU* 6.1 4.9 - - + -
314A VAL* 3.2 12.5 + - + +
315A ALA* 3.0 6.7 + - - +
317A MET* 1.3 84.0 - - + +
319A ASP* 1.3 60.0 + - + +
338A SER* 4.5 0.7 - - - -
339A LEU* 4.1 14.3 - - + +
340A LYS* 3.0 34.7 + - + +
1440A MET* 4.7 12.8 - - + -
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Residues in contact with ASP 319 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97A VAL* 4.2 18.4 - - + +
315A ALA 2.5 26.0 + - - +
316A THR* 3.1 9.2 - - - -
317A MET 3.5 0.2 - - - -
318A VAL* 1.3 77.4 - - + +
320A ASN* 1.3 61.4 + - - +
321A GLU* 3.0 19.3 + - - +
322A LEU* 3.5 28.0 + - - +
323A PRO* 5.6 1.0 - - - +
338A SER* 4.1 2.8 + - - -
340A LYS* 2.9 47.3 + - + +
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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
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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