Contacts of the strand formed by residues 317 - 322 (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 LEU 317 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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303A THR* 4.0 9.2 - - + -
304A HIS 4.0 3.6 - - - -
305A PRO* 3.7 19.3 - - + -
315A ASP 3.7 0.6 - - - -
316A ARG* 1.3 72.5 - - - +
318A ASN* 1.3 62.8 + - - +
332A GLN* 3.4 5.0 - - - -
333A VAL* 2.9 41.1 + - + -
334A SER* 3.1 12.4 + - - -
340A SER* 3.4 19.0 + - - +
341A ALA 3.8 19.3 - - - +
342A TYR 5.4 0.2 - - - +
343A SER* 3.5 38.1 - - - +
354A CYS* 4.3 3.1 - - - -
356A HIS* 3.9 29.2 - - + +
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Residues in contact with ASN 318 (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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302A PHE 3.7 0.5 - - - +
303A THR* 3.0 9.0 - - - -
304A HIS 2.8 42.3 + - - +
306A LEU* 4.2 26.3 - - + +
316A ARG 3.2 5.0 + - - +
317A LEU* 1.3 75.3 - - - +
319A LEU* 1.3 71.8 + - - +
320A TRP* 3.6 19.4 - - - +
329A ASN* 2.4 35.6 + - - +
331A GLY* 3.3 19.4 + - - -
332A GLN* 3.5 7.8 + - - +
333A VAL* 4.8 0.7 - - - -
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Residues in contact with LEU 319 (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 LEU* 4.3 17.9 - - + -
302A PHE 3.5 7.2 - - - +
303A THR* 3.9 14.4 - - + -
318A ASN* 1.3 78.3 + - - +
320A TRP* 1.3 71.6 + - - +
329A ASN* 3.7 0.2 - - - +
330A VAL* 2.8 55.6 + - + -
331A GLY 2.9 13.7 + - - +
333A VAL* 3.7 16.2 - - + -
345A VAL* 4.6 9.0 - - + -
352A LEU* 4.3 3.8 - - + -
371A LEU* 4.3 13.7 - - + -
374A GLU* 4.0 19.3 - - + -
378A ILE* 4.2 9.6 - - + -
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Residues in contact with TRP 320 (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 VAL* 6.2 0.2 - - + -
274A TRP* 3.4 31.3 - - + +
301A LEU* 3.5 6.1 - - - +
302A PHE* 2.9 55.1 + + + +
304A HIS* 4.7 4.8 + - - +
306A LEU* 4.9 2.4 - - + +
318A ASN* 3.6 35.0 + - + +
319A LEU* 1.3 80.4 - - - +
321A LEU* 1.3 62.4 + - - +
322A THR* 6.0 1.1 - - + -
327A ILE* 3.8 17.5 - - + -
328A TYR 3.2 22.2 - - - +
329A ASN* 3.7 18.4 - - + -
330A VAL* 4.1 3.1 - - - -
472A ASN* 3.4 43.7 - - + -
474A ARG* 3.7 31.0 - - + -
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Residues in contact with LEU 321 (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 VAL* 3.6 42.2 - - + -
300A MET 3.3 4.5 - - - +
301A LEU* 3.9 14.1 - - + -
320A TRP* 1.3 76.6 - - - +
322A THR* 1.3 63.7 + - - +
326A ARG 3.9 0.3 - - - +
327A ILE* 3.7 0.7 - - - +
328A TYR* 2.9 37.5 + - + +
330A VAL* 4.1 13.2 - - + -
378A ILE* 4.0 28.0 - - + -
381A VAL* 4.0 22.4 - - + -
382A LEU* 4.1 8.7 - - + -
385A TRP* 3.9 20.6 - - + -
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Residues in contact with THR 322 (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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270A LEU* 4.0 19.6 - - + +
274A TRP* 5.0 8.5 - - + -
289A PHE* 5.6 1.6 - - + -
299A VAL* 3.6 3.6 - - - +
300A MET* 2.8 58.2 + - + +
302A PHE* 6.1 2.9 - - + -
320A TRP* 6.0 0.7 - - + -
321A LEU* 1.3 77.5 - - - +
323A ASP* 1.3 56.9 + - - +
324A ASN* 2.9 19.1 + - - +
325A GLN 3.7 0.5 + - - -
326A ARG 2.8 20.4 + - - -
327A ILE* 3.6 18.0 - - - +
385A TRP* 4.1 6.3 - - - -
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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