Contacts of the helix formed by residues 298 - 311 (chain A) in PDB entry 1MKP
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 SER 298 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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296A GLY* 3.6 1.4 - - - -
297A ILE* 1.3 79.0 + - - +
299A ARG* 1.3 55.4 + - - +
301A VAL* 3.3 7.8 - - - +
302A THR* 2.6 38.5 + - - -
332A PRO* 3.6 5.2 - - - +
333A ASN* 3.0 50.1 + - - -
336A PHE* 3.8 16.8 - - - -
500A CL 4.1 5.4 - - - +
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Residues in contact with ARG 299 (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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239A VAL* 3.5 31.6 - - + +
241A PRO* 3.7 22.9 - - - +
260A ILE* 3.8 24.5 - - - +
261A SER 4.1 3.6 + - - -
262A ASP* 3.6 31.7 + - - +
268A LEU* 4.1 8.2 - - + +
295A ALA* 4.5 3.8 - - - +
298A SER* 1.3 76.3 - - - +
300A SER* 1.3 61.5 + - - +
302A THR* 3.6 5.9 - - - -
303A VAL* 3.1 29.8 + - - +
336A PHE* 3.5 31.8 - - + -
500A CL 3.4 25.1 - - + +
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Residues in contact with SER 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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216A LEU* 3.6 15.3 - - - -
217A GLY 3.9 3.0 + - - -
239A VAL* 3.7 12.2 - - - +
291A VAL* 3.6 31.1 - - - +
292A HIS* 4.2 5.6 - - - -
293A SER* 4.2 1.8 - - - -
296A GLY 3.8 5.9 + - - -
297A ILE* 3.0 32.4 + - - +
299A ARG* 1.3 75.9 - - - +
301A VAL* 1.3 56.6 + - - +
303A VAL 3.1 2.1 + - - -
304A THR* 2.9 30.1 + - - -
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Residues in contact with VAL 301 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
216A LEU* 3.6 11.6 - - + +
297A ILE 2.9 27.4 + - - +
298A SER* 3.3 12.6 - - - +
300A SER* 1.3 76.5 + - - +
302A THR* 1.3 63.2 + - - +
304A THR* 3.6 2.0 - - - -
305A VAL* 2.8 38.0 + - + +
320A TYR* 4.3 7.9 - - + -
323A VAL* 3.9 18.8 - - + -
330A ILE* 3.4 31.4 - - + -
332A PRO* 4.0 18.2 - - + -
501A MPD 4.8 5.2 - - + -
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Residues in contact with THR 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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268A LEU* 3.8 13.5 - - + -
272A PHE* 3.8 22.9 - - + -
298A SER 2.6 23.1 + - - -
299A ARG 3.6 5.4 - - - -
301A VAL* 1.3 77.8 - - - +
303A VAL* 1.3 59.5 - - - +
305A VAL* 3.4 0.4 + - - -
306A ALA* 3.0 27.4 + - - +
336A PHE* 3.3 36.9 - - + +
339A GLN* 5.9 0.4 - - + -
340A LEU* 3.8 18.7 - - + +
501A MPD 3.8 8.9 - - - +
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Residues in contact with VAL 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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237A LEU* 4.1 14.1 - - + -
239A VAL* 4.1 18.6 - - + -
258A ILE* 5.4 1.3 - - + -
268A LEU* 4.3 18.6 - - + -
271A PHE* 6.4 0.9 - - + -
272A PHE* 4.4 11.2 - - + -
275A ALA* 3.8 28.3 - - + -
276A ILE* 5.3 1.9 - - + +
279A ILE* 4.4 9.2 - - + -
291A VAL* 4.1 8.3 - - + -
299A ARG 3.1 18.7 + - - +
300A SER 3.6 4.3 - - - +
302A THR* 1.3 77.0 - - - +
304A THR* 1.3 61.3 + - - +
306A ALA* 3.4 6.8 + - - +
307A TYR* 3.0 21.8 + - - +
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Residues in contact with THR 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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210A ILE* 4.2 22.2 - - + -
214A LEU* 4.4 18.3 - - + +
215A TYR 5.2 0.2 + - - -
216A LEU* 3.5 17.3 - - + +
279A ILE* 5.2 3.6 - - - -
291A VAL* 4.0 13.6 - - - +
300A SER 2.9 16.7 + - - -
301A VAL* 3.6 9.4 - - - -
302A THR 3.2 0.2 - - - -
303A VAL* 1.3 75.4 - - - +
305A VAL* 1.3 66.0 + - - +
307A TYR* 3.1 8.8 + - - +
308A LEU* 3.0 23.2 + - + +
323A VAL* 4.2 18.6 - - + -
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Residues in contact with VAL 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 VAL* 2.8 27.3 + - + +
302A THR 3.8 3.6 - - - +
304A THR* 1.3 71.2 - - - +
306A ALA* 1.3 58.2 + - - +
308A LEU* 3.1 10.2 + - - +
309A MET* 2.8 46.7 + - - +
316A MET* 4.0 12.3 - - + +
319A ALA* 3.8 16.4 - - + -
320A TYR* 3.9 30.1 - - + +
323A VAL* 4.0 15.3 - - + -
340A LEU* 4.0 16.6 - - + -
501A MPD 4.4 4.5 - - + -
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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
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272A PHE* 3.8 42.6 - - + -
276A ILE* 4.2 3.6 - - + -
302A THR 3.0 17.9 + - - +
303A VAL* 3.6 5.6 - - + +
304A THR 3.3 0.2 - - - -
305A VAL* 1.3 75.3 - - - +
307A TYR* 1.3 63.4 + - - +
309A MET* 3.2 9.5 + - - +
310A GLN* 3.1 20.6 + - - +
340A LEU* 4.1 1.5 - - + +
343A PHE* 3.5 18.6 - - + -
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Residues in contact with TYR 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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211A LEU* 4.4 5.8 - - + -
214A LEU* 3.7 27.4 - - + -
276A ILE* 3.7 39.5 - - + +
279A ILE* 3.6 38.4 - - + -
280A ASP* 2.7 30.0 + - - -
283A ARG* 2.9 34.4 + - - -
303A VAL 3.0 14.0 + - - +
304A THR* 3.4 8.7 - - - +
306A ALA* 1.3 78.1 - - - +
308A LEU* 1.3 61.6 + - + +
310A GLN* 3.9 1.0 - - - +
311A LYS* 2.9 55.1 + - + +
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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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210A ILE* 4.2 5.4 - - + -
211A LEU* 3.4 38.8 - - + -
214A LEU* 4.2 12.3 - - + -
304A THR* 3.0 18.7 + - + +
305A VAL* 3.6 6.1 - - - +
307A TYR* 1.3 76.2 - - + +
309A MET* 1.3 66.4 + - - +
311A LYS* 4.7 0.2 - - - -
312A LEU* 2.9 40.5 + - + +
313A ASN 3.9 0.2 + - - -
314A LEU* 4.2 1.8 + - + +
319A ALA* 3.4 34.1 - - + +
322A ILE* 3.9 17.7 - - + -
323A VAL* 3.6 21.1 - - + -
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Residues in contact with MET 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 VAL* 2.8 28.1 + - - +
306A ALA* 3.4 7.2 - - - +
308A LEU* 1.3 75.7 - - - +
310A GLN* 1.3 57.8 + - - +
313A ASN* 3.0 9.9 + - - -
314A LEU* 2.8 43.6 + - - +
315A SER 3.8 2.9 - - - +
316A MET* 3.7 29.4 - - - +
319A ALA* 3.5 14.8 - - + -
340A LEU* 3.6 29.4 - - - +
343A PHE* 3.8 17.7 - - + -
344A GLU* 3.7 21.5 - - + -
347A LEU* 3.8 12.6 - - + +
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Residues in contact with GLN 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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273A PRO* 5.9 1.8 - - - +
276A ILE* 3.8 32.4 - - + +
306A ALA 3.1 11.5 + - - +
307A TYR 4.0 0.7 - - - +
309A MET* 1.3 78.4 - - - +
311A LYS* 1.3 67.3 + - - +
313A ASN* 3.4 15.6 + - - -
343A PHE* 3.3 28.4 - - + -
346A THR* 5.9 0.4 - - - +
347A LEU* 3.6 23.9 - - + +
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Residues in contact with LYS 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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211A LEU* 5.5 0.7 - - + -
276A ILE* 6.1 0.9 - - + -
280A ASP* 3.6 27.5 + - - +
283A ARG* 4.3 10.3 - - - +
307A TYR* 2.9 55.2 + - + +
308A LEU* 4.5 0.7 - - - +
310A GLN* 1.3 76.0 - - - +
312A LEU* 1.3 73.9 + - + +
313A ASN* 5.1 1.4 + - - +
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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