Contacts of the strand formed by residues 287 - 297 (chain M) in PDB entry 6G0L
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 PRO 287 (chain M).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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285M HIS 3.7 7.9 - - - +
286M VAL* 1.3 101.8 - - + +
288M GLU* 1.3 60.8 + - - +
289M ARG 4.7 2.5 - - - +
290M ILE* 5.2 4.5 - - + -
309M VAL* 3.7 23.8 - - + -
310M LYS 3.6 6.5 - - - +
311M TRP* 3.6 11.4 - - + -
312M ARG* 3.3 13.3 + - - +
327M ILE* 5.5 11.7 - - + -
330M LEU* 4.4 11.9 - - + -
331M ALA* 3.8 28.0 - - + -
334M GLN* 4.5 14.2 + - + -
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Residues in contact with GLU 288 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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287M PRO* 1.3 76.4 - - - +
289M ARG* 1.3 69.1 + - + +
310M LYS* 2.7 22.4 + - - +
311M TRP 2.8 20.1 - - - +
312M ARG* 3.3 27.9 - - + +
313M ARG* 4.1 6.8 + - - -
334M GLN* 3.1 26.6 + - - +
441M LEU* 5.5 7.3 - - - +
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Residues in contact with ARG 289 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
288M GLU* 1.3 85.2 + - + +
290M ILE* 1.3 76.5 + - - +
291M ILE* 4.0 4.0 - - + +
309M VAL* 4.3 0.7 - - - +
310M LYS* 2.8 47.6 + - + +
334M GLN* 3.2 43.4 + - - +
337M HIS* 3.2 32.9 + - - +
338M PHE* 3.2 23.0 - - - +
341M ARG* 3.4 41.0 - - - +
452M ASN* 5.7 1.2 - - - +
453M CYS* 6.4 1.8 - - - -
454M ILE* 4.0 17.3 - - + -
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Residues in contact with ILE 290 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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287M PRO* 5.2 3.1 - - + -
289M ARG* 1.3 86.7 - - - +
291M ILE* 1.3 54.1 + - - +
292M ASP 3.6 21.5 - - - +
307M TYR* 3.6 26.0 - - + -
308M LEU 3.7 2.2 - - - +
309M VAL* 4.0 28.7 - - + -
327M ILE* 4.5 14.8 - - + -
334M GLN* 4.1 27.1 - - + +
335M VAL* 5.0 2.7 - - - +
338M PHE* 3.3 26.5 - - + -
341M ARG* 2.4 35.7 + - - -
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Residues in contact with ILE 291 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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289M ARG* 5.1 5.2 - - + -
290M ILE* 1.3 77.0 - - - +
292M ASP* 1.3 71.4 + - - +
308M LEU* 2.8 43.1 + - + +
310M LYS* 4.3 22.7 - - + -
316M TYR* 4.7 13.7 - - + +
319M ALA* 4.7 9.2 - - + -
338M PHE* 3.5 10.1 - - - -
341M ARG* 3.6 6.5 + - - +
454M ILE* 5.9 5.6 - - + -
465M THR* 3.8 24.9 - - + -
469M TYR* 3.7 38.8 - - + -
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Residues in contact with ASP 292 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
290M ILE* 3.6 8.5 - - - +
291M ILE* 1.3 97.3 - - - +
293M SER* 1.3 65.9 + - - +
294M GLN* 4.2 4.0 - - + +
307M TYR* 3.6 0.3 - - - -
308M LEU* 2.9 39.2 + - + +
321M TRP* 5.7 4.7 - - + +
338M PHE* 4.2 4.0 - - - -
468M GLU* 4.3 19.7 - - - +
469M TYR* 3.4 21.3 - - - +
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Residues in contact with SER 293 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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292M ASP* 1.3 79.4 - - - +
294M GLN* 1.3 62.0 + - - +
305M LEU* 3.7 13.8 - - - +
306M GLN 3.5 7.2 - - - -
307M TYR* 3.5 26.5 - - - -
338M PHE* 3.3 25.7 - - - -
342M GLU* 4.1 4.9 + - - -
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Residues in contact with GLN 294 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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292M ASP* 4.2 3.1 - - + -
293M SER* 1.3 77.3 - - - +
295M ARG* 1.3 80.6 + - - +
296M ALA* 3.3 3.7 + - - -
305M LEU* 3.6 2.7 - - - -
306M GLN* 3.3 23.2 + - - +
321M TRP* 4.1 32.1 - - + -
472M TYR* 5.9 3.5 - - - -
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Residues in contact with ARG 295 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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294M GLN* 1.3 86.9 + - - +
296M ALA* 1.3 58.0 + - - +
297M SER 4.3 0.3 + - - -
303M SER* 3.0 40.4 + - - -
304M GLN 3.4 18.4 - - - +
305M LEU* 3.5 24.1 - - + +
1199M ARG* 2.5 66.4 + - - +
1200M ASP* 2.5 26.4 + - - +
1207M THR* 3.4 29.8 + - - +
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Residues in contact with ALA 296 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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294M GLN* 3.3 3.5 + - + +
295M ARG* 1.3 73.7 - - - +
297M SER* 1.3 67.6 + - - +
298M LEU* 3.8 4.2 - - - +
303M SER* 4.2 2.9 - - - -
304M GLN 3.0 31.6 + - - +
306M GLN* 4.5 12.2 + - - +
321M TRP* 3.9 29.6 - - + -
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Residues in contact with SER 297 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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295M ARG 4.3 0.4 + - - -
296M ALA* 1.3 82.1 - - - +
298M LEU* 1.3 79.0 + - - +
301M GLY* 4.0 9.7 + - - -
302M THR 3.2 13.4 + - - -
303M SER* 3.9 8.5 - - - +
306M GLN* 5.6 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