Contacts of the strand formed by residues 347 - 352 (chain D) in PDB entry 1MK9
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 VAL 347 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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306D LYS* 4.1 37.5 + - + +
307D THR* 5.5 2.7 - - + -
338D MET* 3.4 34.8 - - + -
339D ARG 3.3 7.6 - - - +
340D VAL* 3.8 10.5 - - + +
345D LYS 3.3 3.7 + - - +
346D GLU* 1.3 80.6 - - - +
348D ILE* 1.3 64.4 + - - +
349D GLN 3.0 28.5 - - - +
350D GLU* 4.2 10.3 - - + +
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Residues in contact with ILE 348 (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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328D ARG* 3.5 31.4 - - - +
339D ARG* 2.6 47.2 + - - +
340D VAL 5.1 0.2 - - - -
341D ASP* 4.1 24.0 - - + +
346D GLU 3.5 9.6 - - - +
347D VAL* 1.3 79.7 - - - +
349D GLN* 1.3 61.0 + - + +
374H GLN* 6.2 0.4 - - - +
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Residues in contact with GLN 349 (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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337D VAL 4.8 0.2 - - - -
338D MET* 3.3 0.5 - - - -
339D ARG* 3.1 55.7 + - + +
347D VAL* 3.0 19.2 - - - +
348D ILE* 1.3 81.9 - - + +
350D GLU* 1.3 64.8 + - - +
351D TRP* 2.8 51.4 - - + +
375D ASP* 5.0 10.1 + - - -
378D TYR* 5.1 0.9 - - - -
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Residues in contact with GLU 350 (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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306D LYS* 4.7 17.8 + - - +
336D CYS* 4.5 16.4 - - - +
337D VAL 3.5 5.8 - - - +
338D MET* 3.9 19.6 - - + +
347D VAL* 4.2 7.9 - - + +
349D GLN* 1.3 86.6 + - - +
351D TRP* 1.3 71.6 + - - +
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Residues in contact with TRP 351 (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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330D LEU* 5.6 0.2 - - + -
336D CYS* 3.0 10.0 - - - +
337D VAL* 2.7 73.7 + - + +
339D ARG* 3.9 18.2 - - + -
349D GLN* 2.8 46.9 - - + +
350D GLU* 1.3 81.4 - - - +
352D SER* 1.3 59.9 + - - +
355D ASN* 6.0 0.7 - - + -
368D LEU* 5.8 0.7 - - + -
370D PHE* 3.2 52.6 - + + -
372D ASP* 5.8 0.8 + - - -
375D ASP* 5.2 7.9 + - + +
378D TYR* 3.7 37.9 - + + -
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Residues in contact with SER 352 (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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303B ARG* 4.8 16.6 + - - +
304B SER* 5.5 1.7 - - - -
335D GLU 3.6 7.6 - - - -
336D CYS* 4.6 1.1 - - - -
337D VAL* 5.1 0.4 - - - -
351D TRP* 1.3 73.6 - - - +
353D LEU* 1.3 66.1 + - - +
354D THR* 3.8 17.9 - - - -
355D ASN* 2.9 35.4 + - - +
356D ILE* 3.9 7.0 + - - +
370D PHE* 4.0 1.6 - - - -
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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