Contacts of the helix formed by residues 300 - 313 (chain A) in PDB entry 5K6S
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 LYS 300 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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257A VAL 5.0 1.2 + - - -
258A LYS* 3.1 38.2 + - - +
260A LEU* 5.6 9.5 - - + +
261A SER* 4.5 10.8 - - - +
294A PRO* 4.3 13.5 - - + -
298A SER* 2.9 16.2 + - - +
299A PRO* 1.3 74.5 - - - +
301A GLU* 1.3 64.1 + - - +
302A VAL 3.1 0.2 - - - -
303A MET* 3.2 40.6 + - + +
304A PHE* 3.5 13.3 + - + -
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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
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293A TRP* 3.2 31.5 + - + +
294A PRO* 4.0 25.9 - - + +
297A HIS* 3.0 43.7 + - - +
298A SER 2.9 17.2 + - - +
300A LYS* 1.3 76.9 - - - +
302A VAL* 1.3 59.0 + - - +
304A PHE* 3.1 7.5 + - - +
305A LEU* 2.8 33.7 + - + +
330A GLN* 4.3 2.1 - - - +
334A CYS* 3.5 14.7 - - - -
342A VAL* 3.9 24.2 - - + +
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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
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299A PRO* 3.1 17.0 + - + +
301A GLU* 1.3 77.5 - - - +
303A MET* 1.3 63.5 + - - +
305A LEU* 3.4 9.5 + - - +
306A ASN* 3.0 32.1 + - - +
341A GLN* 3.8 37.0 - - + +
342A VAL* 4.1 11.2 - - + +
345A ARG* 4.1 17.7 - - + +
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Residues in contact with MET 303 (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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260A LEU* 4.4 9.4 - - + -
261A SER* 3.6 45.3 - - - +
264A HIS* 3.0 56.1 - - + +
265A PRO* 6.1 0.2 - - + -
299A PRO 4.2 3.0 + - - +
300A LYS* 3.2 34.1 + - + +
301A GLU 3.1 0.4 - - - -
302A VAL* 1.3 78.5 - - - +
304A PHE* 1.3 64.4 + - + +
306A ASN* 3.2 6.2 + - - +
307A GLU 3.0 10.2 + - - -
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Residues in contact with PHE 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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255A HIS* 4.0 36.1 - + + -
260A LEU* 3.8 20.0 - - + -
264A HIS* 4.6 1.8 - + - -
289A LEU* 3.8 42.5 - - + +
292A TYR* 3.7 21.3 - - + -
293A TRP* 3.7 25.3 - + + -
294A PRO* 3.6 23.1 - - + -
300A LYS* 3.6 16.4 - - + -
301A GLU 3.1 7.2 + - - +
303A MET* 1.3 78.8 - - + +
305A LEU* 1.3 61.5 + - - +
307A GLU* 3.2 9.3 + - - +
308A LEU* 2.8 31.0 + - - +
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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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293A TRP* 3.6 23.8 - - + -
301A GLU 2.8 21.4 + - - +
302A VAL* 3.7 4.7 - - - +
304A PHE* 1.3 75.4 - - - +
306A ASN* 1.3 62.8 + - - +
308A LEU* 4.3 0.9 - - + -
309A GLU* 3.1 12.5 + - - +
331A LEU* 4.0 22.9 - - + -
334A CYS* 4.0 6.7 - - - -
342A VAL* 3.5 39.5 - - + +
345A ARG* 3.7 18.6 + - + -
346A ALA* 3.9 12.6 - - + +
349A TYR* 2.8 38.0 + - + +
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Residues in contact with ASN 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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264A HIS* 4.9 4.5 - - + -
302A VAL* 3.0 21.4 + - - +
303A MET* 3.2 10.9 + - - +
305A LEU* 1.3 74.3 - - - +
307A GLU* 1.3 64.2 + - - +
309A GLU* 3.5 2.9 + - - +
310A GLU* 3.2 42.6 + - - +
345A ARG* 3.0 38.7 + - - +
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Residues in contact with GLU 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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255A HIS* 2.7 39.4 + - - -
264A HIS* 2.9 32.5 + - + +
268A ALA* 3.8 21.1 - - + +
271A VAL* 3.9 15.5 - - + +
272A VAL* 5.0 0.6 - - + +
289A LEU* 3.6 22.6 - - + +
303A MET 3.0 5.7 + - - -
304A PHE* 3.2 11.0 + - - +
306A ASN* 1.3 77.2 - - - +
308A LEU* 1.3 61.6 + - - +
310A GLU* 3.4 11.9 + - - +
311A ILE* 3.1 28.0 + - + +
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Residues in contact with LEU 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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286A VAL* 4.7 20.2 - - + +
289A LEU* 4.1 27.1 - - + +
290A LEU* 5.0 6.7 - - + -
293A TRP* 3.7 27.1 - - + -
304A PHE 2.8 16.6 + - - +
305A LEU* 4.3 1.8 - - + -
307A GLU* 1.3 76.3 - - - +
309A GLU* 1.3 59.1 + - - +
311A ILE* 3.5 11.3 + - + +
312A LEU* 3.1 31.8 + - + +
327A LEU* 3.7 35.9 - - + +
330A GLN* 6.1 0.7 - - + -
331A LEU* 5.7 1.6 - - + -
349A TYR* 3.3 16.2 - - + +
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Residues in contact with GLU 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 3.1 15.7 + - - +
306A ASN 3.9 1.3 - - - +
308A LEU* 1.3 74.4 - - - +
310A GLU* 1.3 62.8 + - + +
311A ILE 3.2 0.7 - - - -
312A LEU* 3.3 6.9 + - - +
313A ASP* 3.1 38.7 + - - +
345A ARG* 2.5 47.0 + - - +
348A TYR* 4.3 14.1 - - - +
349A TYR* 3.5 19.3 + - + -
351A ASN 5.8 0.2 - - - -
352A ASN* 3.8 23.1 + - - +
355A ILE* 4.2 15.9 - - + -
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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
----------------------------------------------------------
264A HIS* 5.9 0.2 - - - -
268A ALA* 3.7 26.0 - - - +
269A TYR* 5.7 0.3 - - - -
272A VAL* 3.8 18.7 - - + +
306A ASN* 3.2 32.2 + - - +
307A GLU* 3.7 5.2 - - - +
308A LEU 3.3 0.2 - - - -
309A GLU* 1.3 77.4 - - + +
311A ILE* 1.3 61.1 + - - +
313A ASP* 3.7 18.6 + - - +
314A VAL* 3.7 15.9 - - - +
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Residues in contact with ILE 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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271A VAL* 4.1 9.4 - - + -
272A VAL* 4.3 12.3 - - + -
275A LEU* 3.7 24.4 - - + +
282A THR* 5.9 0.4 - - + -
285A VAL* 3.8 20.2 - - + -
286A VAL* 4.4 17.0 - - + -
289A LEU* 3.7 30.5 - - + -
307A GLU* 3.1 15.1 + - + +
308A LEU* 3.6 13.0 - - + +
309A GLU 3.2 0.2 - - - -
310A GLU* 1.3 77.3 - - - +
312A LEU* 1.3 66.5 + - + +
313A ASP 3.1 0.7 - - - -
314A VAL* 3.2 18.9 + - - +
315A ILE* 3.3 20.9 + - + +
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Residues in contact with LEU 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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286A VAL* 6.5 0.4 - - + -
308A LEU* 3.1 18.0 + - + +
309A GLU* 3.3 8.0 + - - +
311A ILE* 1.3 81.4 - - + +
313A ASP* 1.3 61.8 + - - +
315A ILE* 3.2 20.5 - - + +
320A PHE* 3.8 28.9 - - + -
323A ILE* 5.4 0.2 - - + -
327A LEU* 3.8 33.7 - - + -
328A PHE* 5.7 2.9 - - + -
349A TYR* 3.7 28.3 - - + -
354A TYR* 3.2 24.2 - - - -
355A ILE* 3.9 28.5 - - + -
358A LEU* 4.5 2.1 - - + +
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Residues in contact with ASP 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 GLU* 3.1 22.8 + - - +
310A GLU* 3.7 18.4 - - - +
311A ILE 3.1 0.6 - - - -
312A LEU* 1.3 77.2 - - - +
314A VAL* 1.3 66.1 + - + +
315A ILE 3.6 0.2 - - - -
352A ASN* 2.8 35.5 + - - +
354A TYR* 4.0 18.3 - - - +
355A ILE* 5.2 0.3 - - - +
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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
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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