Contacts of the strand formed by residues 297 - 305 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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293A THR* 3.6 3.8 - - - +
294A ILE 3.1 29.7 + - - +
295A GLU 3.3 3.3 - - - +
296A GLY* 1.3 77.7 - - - +
298A ARG* 1.3 76.1 + - - +
299A VAL* 3.2 13.2 + - + +
323A ASP* 5.0 7.6 - - + +
326A ARG* 6.1 0.9 - - - -
382A LEU* 3.2 52.9 - - + +
385A TRP* 4.1 15.7 - - + -
386A LYS* 3.7 27.4 - - + +
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Residues in contact with ARG 298 (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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235A GLU 5.0 5.3 + - - -
236A TRP* 3.4 33.6 - - + -
291A ALA* 3.7 33.5 + - - +
292A VAL* 3.4 16.9 - - - +
293A THR* 3.0 26.0 + - - +
296A GLY 4.0 2.4 + - - -
297A MET* 1.3 76.9 - - - +
299A VAL* 1.3 63.4 + - - +
323A ASP* 4.7 3.8 - - - +
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Residues in contact with VAL 299 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
236A TRP* 3.9 4.7 - - - -
291A ALA* 3.2 7.1 - - - +
292A VAL* 2.7 58.5 + - + +
294A ILE* 4.2 11.7 - - + -
297A MET* 3.2 16.6 + - + +
298A ARG* 1.3 79.7 - - - +
300A MET* 1.3 65.4 + - - +
301A LEU* 4.7 0.9 - - + -
321A LEU* 3.6 21.8 - - + -
322A THR 3.6 10.3 - - - +
323A ASP* 4.8 2.0 - - + -
382A LEU* 3.7 30.7 - - + -
385A TRP* 4.8 4.3 - - + -
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Residues in contact with MET 300 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
234A LEU* 3.4 39.7 - - + -
236A TRP* 3.7 32.3 - - + -
241A ILE* 4.1 6.3 - - + -
270A LEU* 4.4 4.3 - - + -
289A PHE* 3.9 17.7 - - + -
290A THR 3.2 4.5 - - - +
291A ALA* 4.5 0.7 - - - -
299A VAL* 1.3 77.5 - - - +
301A LEU* 1.3 64.0 + - - +
302A PHE* 4.3 0.4 + - - -
320A TRP 3.9 0.2 - - - +
321A LEU* 3.3 6.6 - - - +
322A THR* 2.8 51.5 + - + +
324A ASN* 3.7 42.2 - - + +
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Residues in contact with LEU 301 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
288A SER* 3.6 1.8 + - - +
289A PHE* 3.2 7.8 + - - -
290A THR* 3.0 38.1 + - - +
292A VAL* 4.0 26.0 - - + -
294A ILE* 4.8 5.4 - - + -
299A VAL* 4.7 2.7 - - + -
300A MET* 1.3 73.0 - - - +
302A PHE* 1.3 60.7 + - - +
303A THR* 6.1 0.2 - - - -
319A LEU* 4.3 10.3 - - + -
320A TRP 3.5 9.6 - - - +
321A LEU* 3.9 26.2 - - + -
345A VAL* 4.0 17.8 - - + +
347A TYR* 4.9 1.3 - - + -
352A LEU* 3.9 28.9 - - + -
378A ILE* 3.9 21.3 - - + -
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Residues in contact with PHE 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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243A ASN* 3.1 30.5 - - - -
251A ARG* 3.5 21.1 - - - -
274A TRP* 3.4 54.7 - + + -
287A SER* 3.5 27.4 - - - -
288A SER 3.2 15.0 - - - -
289A PHE* 3.8 15.3 - + + -
300A MET 4.3 0.9 + - - +
301A LEU* 1.3 74.9 - - - +
303A THR* 1.3 62.2 + - - +
304A HIS* 3.6 21.5 - - + -
319A LEU* 3.5 2.7 - - - +
320A TRP* 2.9 48.1 + + + +
322A THR* 6.1 2.9 - - + -
345A VAL* 5.9 0.2 - - - -
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Residues in contact with THR 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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286A GLN 5.4 0.2 - - - -
287A SER* 2.9 26.7 + - - -
288A SER* 3.0 22.4 + - - -
302A PHE* 1.3 80.1 - - - +
304A HIS* 1.3 64.2 + - - +
317A LEU* 4.0 10.3 - - + -
318A ASN 3.0 12.8 - - - +
319A LEU* 3.9 14.8 - - + -
333A VAL* 5.4 2.0 - - + -
343A SER* 2.7 29.3 + - - +
345A VAL* 3.6 26.9 - - + -
354A CYS* 5.3 1.1 - - - -
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Residues in contact with HIS 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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251A ARG* 3.5 34.4 - - - +
274A TRP* 5.5 3.6 - - + -
275A GLY 4.2 6.4 + - - -
276A PRO* 3.6 33.0 - - + +
284A GLY* 4.6 0.9 - - - -
285A SER* 3.8 20.9 + - - -
286A GLN 5.2 0.2 - - - -
287A SER* 3.7 10.8 - - - -
302A PHE* 3.6 17.0 - - + -
303A THR* 1.3 77.2 - - - +
305A PRO* 1.3 109.2 + - + +
306A LEU* 4.7 2.2 - - - +
307A ASN* 5.6 0.2 - - + -
314A ARG* 6.3 0.2 - - + -
317A LEU* 4.0 2.0 - - - -
318A ASN* 2.8 32.1 + - - +
320A TRP* 4.7 4.9 + - - +
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Residues in contact with PRO 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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276A PRO 4.2 0.7 - - - +
285A SER* 3.7 28.3 - - - +
286A GLN 4.6 1.3 - - - +
304A HIS* 1.3 127.0 + - + +
306A LEU* 1.3 63.9 + - - +
307A ASN* 4.3 0.6 - - + +
314A ARG* 3.8 31.2 - - + +
315A ASP 3.7 11.9 - - - +
316A ARG 3.4 7.6 - - - +
317A LEU* 3.7 6.5 - - + -
340A SER 3.8 9.0 - - - +
341A ALA 3.8 13.2 - - - +
471A GLN* 4.5 0.7 + - - -
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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