Contacts of the helix formed by residues 301 - 319 (chain A) in PDB entry 4PK7
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 ILE 301 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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159A TYR* 5.8 0.7 - - - +
213A ARG* 3.3 53.2 - - + +
216A ARG* 3.7 11.2 - - - +
217A HIS* 5.9 1.3 - - - +
299A ASP* 2.8 17.3 + - - +
300A ALA* 1.3 83.4 - - + +
302A ALA* 1.3 66.5 - - - +
303A GLU* 3.8 19.3 - - + +
304A ILE* 3.2 24.1 + - + +
305A ARG* 3.3 15.3 + - - +
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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
----------------------------------------------------------
300A ALA 3.5 1.4 + - - -
301A ILE* 1.3 73.1 - - - +
303A GLU* 1.3 66.9 + - - +
305A ARG* 3.0 32.5 + - - +
306A ALA* 2.9 21.7 + - - +
340A GLN* 3.6 26.5 - - + +
342A GLU* 4.5 8.1 - - + +
343A VAL* 3.5 9.9 - - + +
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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
----------------------------------------------------------
159A TYR* 5.1 0.3 + - - -
161A LEU 3.6 13.2 - - - +
162A THR* 3.9 13.1 - - - +
217A HIS* 3.5 33.2 + - + +
301A ILE* 3.3 12.8 - - + +
302A ALA* 1.3 78.1 - - - +
304A ILE* 1.3 61.8 + - - +
306A ALA* 3.6 5.0 + - - +
307A ILE* 3.3 25.8 + - + +
342A GLU* 4.1 24.4 + - - +
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Residues in contact with ILE 304 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
213A ARG* 5.0 2.5 - - + -
216A ARG* 4.1 14.1 - - + +
217A HIS* 3.7 46.0 - - + +
220A THR* 4.1 21.1 - - + -
296A ARG* 3.5 22.7 - - + +
299A ASP* 3.6 28.5 - - + +
301A ILE* 3.2 21.9 + - + +
302A ALA 3.1 0.8 - - - -
303A GLU* 1.3 78.0 - - - +
305A ARG* 1.3 64.0 + - - +
307A ILE* 3.2 17.2 + - + +
308A CYS* 3.3 12.8 + - - -
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Residues in contact with ARG 305 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
296A ARG 4.1 2.7 - - - -
297A TYR 3.0 27.8 - - - +
298A ARG* 3.8 6.1 - - - +
299A ASP 2.7 51.3 + - - +
300A ALA* 2.9 20.4 + - - +
301A ILE 3.5 2.7 - - - +
302A ALA* 3.0 33.0 + - - +
304A ILE* 1.3 76.5 - - - +
306A ALA* 1.3 62.4 + - - +
308A CYS* 3.3 5.2 + - - +
309A ILE* 3.2 25.6 + - - +
335A THR* 5.5 0.7 - - + -
338A ASP* 2.7 43.4 + - - -
339A LYS* 5.0 2.2 - - - +
340A GLN* 3.6 9.9 - - - +
343A VAL* 4.0 12.1 - - + +
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Residues in contact with ALA 306 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
302A ALA 2.9 14.8 + - - +
303A GLU 3.8 5.8 - - - +
305A ARG* 1.3 74.9 - - - +
307A ILE* 1.3 64.8 + - - +
309A ILE* 4.7 0.7 - - - +
310A GLU* 3.0 26.0 + - - +
342A GLU* 4.4 18.4 - - + +
343A VAL* 4.0 19.0 - - + +
346A LYS* 3.9 29.4 - - + +
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Residues in contact with ILE 307 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172A LYS* 6.2 3.6 - - - +
217A HIS* 3.5 37.2 - - + +
220A THR* 4.3 7.2 - - + -
221A LEU* 3.7 44.0 - - + +
224A MET* 3.9 22.7 - - + -
303A GLU* 3.3 13.1 + - + +
304A ILE* 3.2 11.3 + - - +
306A ALA* 1.3 80.1 - - - +
308A CYS* 1.3 63.8 + - - +
310A GLU* 3.3 10.7 + - - +
311A GLU* 3.3 22.1 + - + +
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Residues in contact with CYS 308 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
220A THR* 3.7 17.9 - - - -
224A MET* 4.3 9.6 - - - -
293A PHE* 3.4 32.6 - - + -
296A ARG* 3.6 40.6 - - - -
297A TYR* 3.6 20.2 - - + -
304A ILE 3.3 5.5 + - - -
305A ARG 3.6 3.6 - - - +
306A ALA 3.3 0.4 - - - -
307A ILE* 1.3 80.6 - - - +
309A ILE* 1.3 62.6 + - - +
311A GLU* 3.2 4.5 + - - +
312A ILE 3.1 18.7 + - - -
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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
----------------------------------------------------------
293A PHE* 4.4 12.3 - - + -
297A TYR* 4.5 10.5 - - + +
305A ARG 3.2 14.3 + - - +
306A ALA* 4.2 3.1 - - - +
308A CYS* 1.3 74.9 - - + +
310A GLU* 1.3 67.7 + - - +
312A ILE* 3.3 14.0 - - + +
313A GLY* 3.2 16.1 + - - -
331A TYR 4.5 11.7 - - - +
332A VAL* 4.2 9.9 - - + +
335A THR* 3.4 39.7 - - + +
343A VAL* 4.7 1.1 - - + -
346A LYS* 3.9 19.3 - - + +
347A CYS* 3.8 26.2 - - - +
350A ALA* 4.3 3.2 - - + +
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Residues in contact with GLU 310 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172A LYS* 6.0 0.2 + - - -
225A LYS* 5.3 1.7 + - - -
306A ALA 3.0 19.3 + - - +
307A ILE* 3.4 11.0 - - - +
309A ILE* 1.3 76.5 - - - +
311A GLU* 1.3 76.8 + - - +
313A GLY* 3.1 12.0 + - - -
314A ILE* 3.1 22.5 + - + +
346A LYS* 3.3 40.6 + - + +
349A THR* 5.7 4.2 - - + +
350A ALA* 5.2 1.8 - - - +
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Residues in contact with GLU 311 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
221A LEU* 6.2 0.7 - - + -
224A MET* 3.6 26.6 - - + +
225A LYS* 2.4 36.6 + - - +
228A THR* 2.5 30.3 + - - +
307A ILE* 3.3 10.5 + - + +
308A CYS 3.2 7.5 + - - +
310A GLU* 1.3 84.6 - - - +
312A ILE* 1.3 62.2 + - - +
314A ILE* 3.0 24.7 + - - +
315A TRP* 2.9 52.6 + - + -
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Residues in contact with ILE 312 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
289A PHE* 4.4 1.8 - - + -
293A PHE* 3.7 26.2 - - + -
308A CYS 3.1 11.4 + - - +
309A ILE* 3.3 25.4 - - + +
311A GLU* 1.3 77.2 - - - +
313A GLY* 1.3 65.8 + - - +
315A TRP* 3.5 26.1 + - + +
316A MET* 3.2 25.3 + - + +
328A TYR* 3.5 46.9 - - + +
331A TYR* 4.2 5.8 - - + -
332A VAL* 3.7 23.1 - - + -
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Residues in contact with GLY 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 3.2 1.2 + - - -
310A GLU 3.1 9.5 + - - -
312A ILE* 1.3 84.9 - - - +
314A ILE* 1.3 60.4 + - - +
316A MET* 3.3 12.8 + - - +
317A LYS* 3.1 23.7 + - - +
350A ALA* 3.8 31.4 - - - +
354A LEU* 4.6 2.4 - - - +
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Residues in contact with ILE 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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225A LYS* 5.0 1.8 - - - +
228A THR* 3.7 27.4 - - + -
310A GLU* 3.1 21.3 + - + +
311A GLU* 3.0 36.4 + - - +
313A GLY* 1.3 74.9 - - - +
315A TRP* 1.3 65.3 + - - +
317A LYS* 3.4 9.9 + - + +
318A MET* 3.0 29.3 + - + +
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Residues in contact with TRP 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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224A MET* 3.7 27.4 - - + -
227A MET* 3.3 47.3 - - + -
228A THR* 2.8 36.9 + - + +
231A VAL* 3.8 18.8 - - + -
288A ILE* 5.8 0.2 - - + -
289A PHE* 4.2 14.8 - + - -
293A PHE* 4.0 10.1 - + + -
311A GLU* 2.9 30.7 + - + +
312A ILE* 3.5 35.4 - - + +
313A GLY 3.3 0.2 - - - -
314A ILE* 1.3 77.4 - - - +
316A MET* 1.3 62.2 + - + +
318A MET* 4.1 5.8 - - + -
319A TYR* 3.1 21.5 + - - +
323A PHE* 3.7 32.2 - + + +
328A TYR* 5.0 0.2 - + - -
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Residues in contact with MET 316 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
312A ILE* 3.2 24.7 + - + +
313A GLY* 3.3 15.2 + - - +
314A ILE 3.3 0.2 - - - -
315A TRP* 1.3 77.2 - - - +
317A LYS* 1.3 57.9 + - - +
320A SER* 3.2 29.6 - - - -
323A PHE* 3.3 35.7 - - + +
324A LEU* 4.1 6.5 - - - +
328A TYR* 4.2 8.5 - - + +
329A LEU* 3.4 45.3 - - + -
332A VAL* 4.0 20.2 - - + -
350A ALA* 5.3 2.5 - - + -
351A LEU* 5.9 0.9 - - + -
354A LEU* 3.8 23.2 - - + +
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Residues in contact with LYS 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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313A GLY 3.1 16.5 + - - +
314A ILE* 4.0 9.4 - - - +
316A MET* 1.3 78.1 - - - +
318A MET* 1.3 61.6 + - + +
320A SER* 4.6 4.7 + - - -
353A GLY* 3.2 35.4 - - - +
354A LEU* 3.6 15.7 - - + +
356A TYR 5.0 4.6 + - - +
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Residues in contact with MET 318 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184A ARG* 5.1 4.7 - - - -
228A THR* 3.4 44.4 - - + +
231A VAL* 3.8 24.7 - - + -
232A ASN* 4.2 19.1 - - - +
235A LEU* 3.6 25.3 - - + +
314A ILE* 3.0 24.3 + - + +
315A TRP* 3.4 5.4 + - + +
317A LYS* 1.3 80.5 - - + +
319A TYR* 1.3 59.0 + - - +
320A SER 3.7 1.4 + - - -
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Residues in contact with TYR 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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231A VAL* 3.6 37.2 - - + -
234A ALA* 4.2 11.0 - - + -
235A LEU* 3.9 42.0 - - + -
238A SER* 3.6 23.7 + - - -
315A TRP 3.1 7.2 + - - -
318A MET* 1.3 79.5 - - - +
320A SER* 1.3 63.1 + - - +
321A ASP* 4.2 13.5 - - + -
322A ALA* 3.0 43.4 + - + +
323A PHE* 3.1 18.5 + + + -
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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