Contacts of the strand formed by residues 301 - 306 (chain A) in PDB entry 1MK2
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 GLU 301 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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296A TYR 3.5 0.7 - - - +
297A TYR* 3.3 5.2 - - - -
298A ILE* 2.5 48.1 + - + +
299A GLY 3.0 8.6 - - - +
300A GLY* 1.3 73.1 - - - +
302A VAL* 1.3 61.4 + - - +
303A PHE* 3.9 19.5 - - + -
340A LYS* 2.9 37.6 + - - +
342A PHE 3.4 2.2 - - - +
343A ASN* 3.4 10.8 + - - +
344A ASN* 2.7 36.2 + - - +
345A GLN* 3.8 14.7 + - - +
690B ALA* 5.6 0.9 - - + -
695B ALA* 4.1 17.9 - - + -
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Residues in contact with VAL 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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231A TRP* 3.9 20.4 - - + -
295A LEU* 5.4 1.3 - - + -
296A TYR 3.2 9.9 - - - +
297A TYR* 4.1 17.5 - - + -
300A GLY 4.1 6.7 - - - +
301A GLU* 1.3 80.5 - - - +
303A PHE* 1.3 60.5 + - - +
340A LYS* 3.2 2.8 - - - +
341A ILE* 2.6 58.7 + - + +
342A PHE* 2.9 34.9 + - + -
397A LEU* 5.5 0.4 - - + -
399A LEU* 4.4 15.9 - - + -
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Residues in contact with PHE 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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295A LEU* 3.5 7.3 - - - +
296A TYR* 3.0 36.5 + - + +
298A ILE* 3.9 26.7 - - + -
301A GLU* 3.9 18.6 - - + -
302A VAL* 1.3 81.9 - - - +
304A ALA* 1.3 61.9 + - - +
305A GLU 4.2 0.2 - - - -
338A ASN* 3.8 6.7 - - - -
339A LEU 3.1 7.2 - - - +
340A LYS* 3.6 43.5 - - + -
341A ILE* 4.1 1.8 - - - -
686B PRO* 3.6 33.0 - - + -
689B GLN* 3.3 44.2 - - + -
690B ALA* 4.8 4.5 - - + -
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Residues in contact with ALA 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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293A VAL* 3.9 9.6 - - + -
294A ARG 3.4 5.2 - - - -
295A LEU* 3.9 16.4 - - + -
303A PHE* 1.3 76.8 - - - +
305A GLU* 1.3 62.0 + - - +
306A CYS 3.9 1.3 + - - -
333A ILE* 3.9 17.0 - - + +
338A ASN* 3.1 4.3 - - - -
339A LEU 2.9 25.0 + - - -
341A ILE* 4.0 23.6 - - + -
373A MET* 4.2 7.0 - - + -
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Residues in contact with GLU 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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293A VAL* 3.2 4.1 - - - +
294A ARG* 2.6 42.6 + - + +
296A TYR* 2.5 43.1 + - + -
303A PHE 4.2 0.4 - - - -
304A ALA* 1.3 74.4 - - - +
306A CYS* 1.3 63.3 + - - +
307A LEU* 3.0 22.4 + - + +
336A GLY* 4.2 12.6 - - - +
337A CYS 3.3 17.0 - - - +
338A ASN* 3.7 20.6 + - + -
683B THR 5.4 2.9 - - - +
685B PRO* 5.4 2.4 - - - +
686B PRO* 4.2 5.1 - - - +
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Residues in contact with CYS 306 (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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292A GLY 4.0 3.1 - - - -
304A ALA 3.9 2.6 + - - -
305A GLU* 1.3 70.4 - - - +
307A LEU* 1.3 63.2 + - - +
308A SER* 3.8 7.6 - - - -
310A SER 3.3 26.0 - - - -
312A ILE* 3.6 25.6 - - + +
333A ILE* 3.3 21.1 - - + +
334A PRO 3.3 17.0 - - - +
335A PRO* 3.7 15.0 - - - -
336A GLY* 3.1 24.8 + - - -
337A CYS 2.9 10.3 + - - +
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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