Contacts of the strand formed by residues 297 - 305 (chain B) in PDB entry 1MS4
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 MET 297 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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293B THR* 3.5 2.2 - - - +
294B ILE 3.0 32.5 + - - +
295B GLU* 3.3 4.6 - - + +
296B GLY* 1.3 78.4 - - - +
298B ARG* 1.3 76.7 + - - +
299B VAL* 3.3 15.1 + - + +
323B ASP* 5.3 6.1 - - + +
326B ARG* 6.0 0.9 - - - -
382B LEU* 3.3 49.1 - - + +
385B TRP* 4.3 19.1 - - - -
386B LYS* 3.7 25.6 - - + +
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Residues in contact with ARG 298 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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235B GLU 4.8 5.7 + - - -
236B TRP* 3.4 33.5 - - + -
237B GLU* 6.3 2.0 - - + -
291B ALA* 3.3 34.8 + - - +
292B VAL* 3.4 17.8 - - - +
293B THR* 2.8 35.2 + - - +
296B GLY 3.9 3.0 + - - -
297B MET* 1.3 75.6 - - - +
299B VAL* 1.3 66.5 + - - +
323B ASP* 4.6 3.8 - - - +
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Residues in contact with VAL 299 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
236B TRP* 3.9 6.0 - - - -
291B ALA* 3.2 5.2 - - - -
292B VAL* 2.8 51.9 + - + +
294B ILE* 4.1 13.9 - - + -
297B MET* 3.8 24.2 - - + +
298B ARG* 1.3 81.9 - - - +
300B MET* 1.3 66.3 + - - +
301B LEU* 4.8 0.4 - - + -
321B LEU* 3.8 21.3 - - + -
322B THR 3.8 11.2 - - - +
323B ASP* 4.7 6.5 - - + -
382B LEU* 3.8 21.1 - - + -
385B TRP* 4.8 0.9 - - + -
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Residues in contact with MET 300 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
234B LEU* 3.6 37.5 - - + -
236B TRP* 3.6 28.5 - - + -
241B ILE* 4.3 3.8 - - + -
270B LEU* 4.3 7.0 - - + -
289B PHE* 4.0 17.3 - - + -
290B THR 3.0 6.1 - - - +
291B ALA* 4.6 0.4 - - - -
299B VAL* 1.3 79.1 - - - +
301B LEU* 1.3 63.0 + - - +
302B PHE 4.2 0.2 - - - -
321B LEU* 3.6 8.7 - - - +
322B THR* 2.9 43.0 + - + +
324B ASN* 3.6 49.4 - - + +
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Residues in contact with LEU 301 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
288B SER* 3.7 2.0 + - - +
289B PHE* 3.2 7.0 + - - -
290B THR* 2.9 42.3 + - - +
292B VAL* 4.0 25.4 - - + -
294B ILE* 4.8 10.5 - - + -
299B VAL* 4.8 0.4 - - + -
300B MET* 1.3 74.1 - - - +
302B PHE* 1.3 60.3 + - - +
319B LEU* 4.4 10.5 - - + -
320B TRP 3.6 8.5 - - - +
321B LEU* 3.8 25.8 - - + -
345B VAL* 4.2 14.4 - - + -
347B TYR* 5.1 1.6 - - + -
352B LEU* 3.7 29.6 - - + -
378B ILE* 4.0 20.9 - - + -
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Residues in contact with PHE 302 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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243B ASN* 3.2 30.3 - - - -
251B ARG* 3.7 18.8 - - - -
274B TRP* 3.2 56.1 - + + -
287B SER* 3.5 29.6 - - - -
288B SER 3.3 6.1 - - - -
289B PHE* 3.7 16.8 - + + -
300B MET 4.2 0.9 - - - -
301B LEU* 1.3 75.0 - - - +
303B THR* 1.3 65.0 + - - +
304B HIS* 3.7 18.8 - - + -
319B LEU* 3.6 2.2 - - - +
320B TRP* 2.9 48.2 + + + +
322B THR* 5.8 3.6 - - + -
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Residues in contact with THR 303 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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286B GLN 5.5 0.2 - - - -
287B SER* 2.8 35.7 + - - -
288B SER* 3.0 24.3 + - - -
302B PHE* 1.3 80.5 - - - +
304B HIS* 1.3 56.6 + - - +
317B LEU* 4.1 10.3 - - + -
318B ASN 3.2 10.1 - - - +
319B LEU* 3.7 17.3 - - + -
333B VAL* 5.3 4.0 - - + -
343B SER* 2.7 28.0 + - - +
345B VAL* 3.6 26.9 - - + -
354B CYS* 5.4 0.9 - - - -
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Residues in contact with HIS 304 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
251B ARG* 3.6 29.6 + - - +
274B TRP* 5.4 4.9 - - + -
275B GLY 4.3 4.9 + - - -
276B PRO* 3.7 33.7 - - + +
283B PRO 5.8 0.2 - - - -
284B GLY* 4.6 1.1 - - - -
285B SER* 3.9 19.7 + - - -
286B GLN 5.3 0.2 - - - -
287B SER* 3.5 16.6 - - - -
302B PHE* 3.7 16.1 - + + -
303B THR* 1.3 75.4 - - - +
305B PRO* 1.3 107.3 + - + +
306B LEU* 4.9 1.8 - - - +
307B ASN* 5.7 0.4 - - + -
317B LEU* 4.2 2.2 - - - +
318B ASN* 2.9 33.1 + - - +
320B TRP* 4.8 4.3 + - - +
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Residues in contact with PRO 305 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
285B SER* 3.6 30.1 - - - +
286B GLN 4.8 0.9 - - - +
304B HIS* 1.3 124.0 + - + +
306B LEU* 1.3 64.6 + - - +
307B ASN* 4.1 1.9 - - + +
314B ARG* 3.6 33.4 - - + +
315B ASP 3.5 13.0 - - - +
316B ARG 3.2 8.1 - - - +
317B LEU* 3.8 4.9 - - + -
340B SER 3.9 7.0 - - - +
341B ALA 3.7 13.7 - - - +
471B GLN* 4.3 1.2 + - - -
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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