Contacts of the strand formed by residues 322 - 326 (chain D) in PDB entry 1M54
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 LYS 322 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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276D ARG* 3.3 24.1 - - - +
277D ILE 3.6 2.0 + - - -
278D ILE* 3.6 14.9 - - + -
279D GLY 3.1 22.1 + - - -
320D VAL* 3.5 5.5 + - - +
321D ASP* 1.3 80.4 - - - +
323D TRP* 1.3 81.3 + - - +
324D PHE* 3.9 31.1 - - + -
360D ALA* 5.8 2.2 + - - +
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Residues in contact with TRP 323 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
255D VAL* 3.6 41.5 - - + -
279D GLY 3.6 14.1 - - - -
280D VAL 4.7 0.2 - - - -
281D ASP* 3.8 23.3 - - + -
287D LEU* 4.0 2.9 - - + -
288D ALA* 3.4 32.5 - - + -
289D GLU* 3.5 39.3 - - + +
290D PRO* 5.7 1.9 - - + +
293D LEU* 3.9 22.1 - - + +
315D LEU* 4.2 11.4 - - + -
317D ARG* 4.2 14.5 + - - -
320D VAL* 2.8 46.2 + - + +
322D LYS* 1.3 83.9 - - - +
324D PHE* 1.3 72.7 + - - +
325D LYS* 5.9 0.2 - - + -
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Residues in contact with PHE 324 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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278D ILE* 3.4 16.8 - - + -
279D GLY 3.1 5.6 + - - +
280D VAL* 3.7 2.8 - - - +
281D ASP* 3.1 27.2 + - - +
293D LEU* 5.1 0.9 - - - -
322D LYS* 3.9 30.1 - - + -
323D TRP* 1.3 77.1 - - - +
325D LYS* 1.3 65.9 + - - +
326D SER 3.7 0.2 + - - -
356D VAL* 3.3 38.4 - - + -
359D LYS* 4.5 29.6 - - + -
360D ALA* 3.3 36.1 - - + -
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Residues in contact with LYS 325 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281D ASP* 3.1 9.8 + - - +
282D PRO 3.4 6.3 - - - -
283D GLU* 2.8 59.8 - - + +
284D GLY 5.0 0.7 - - - +
285D SER 4.7 0.4 - - - -
288D ALA* 4.6 9.9 - - + -
293D LEU* 3.3 61.2 - - + +
294D ASN* 4.2 18.4 - - - +
296D THR* 5.8 0.2 - - - -
324D PHE* 1.3 80.9 - - - +
326D SER* 1.3 61.6 + - - +
327D ASN* 5.3 0.2 - - - +
330D GLU* 4.0 5.5 - - - +
356D VAL* 5.0 3.3 - - - +
359D LYS* 5.5 4.0 + - - -
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Residues in contact with SER 326 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
280D VAL* 3.7 18.4 - - - -
281D ASP 2.5 11.3 + - - -
282D PRO* 2.7 32.6 - - - +
283D GLU* 3.3 23.1 + - - +
303D VAL* 5.8 0.7 - - - +
306D ILE* 4.1 0.3 - - - +
324D PHE 3.7 1.0 + - - -
325D LYS* 1.3 77.3 - - - +
327D ASN* 1.3 69.7 + - - +
330D GLU* 3.4 6.1 - - - -
352D SER* 3.4 25.4 + - - -
356D VAL* 5.1 3.1 - - - -
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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
------------------------------------------------------------
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