Contacts of the strand formed by residues 253 - 257 (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 SER 253 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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251A GLN 3.4 0.8 - - - -
252A PRO* 1.3 87.9 - - - +
254A MET* 1.3 54.6 + - - +
266A GLU* 2.3 24.9 - - - +
294A ARG* 3.3 33.1 + - - -
295A LEU 3.2 4.0 - - - -
296A TYR* 3.5 21.7 - - - -
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Residues in contact with MET 254 (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* 4.5 8.1 - - + -
234A ILE* 3.3 26.7 - - + -
247A PHE* 3.2 33.0 - - + -
249A ALA* 3.7 28.3 - - - -
251A GLN 5.1 3.1 - - - +
253A SER* 1.3 74.8 - - - +
255A THR* 1.3 78.3 + - - +
256A VAL* 3.9 5.6 - - + -
265A SER 4.7 2.5 - - - +
266A GLU* 3.3 29.4 - - - +
268A PHE* 4.1 0.4 - - + -
294A ARG* 3.2 8.8 - - - +
295A LEU* 2.6 50.3 + - + +
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Residues in contact with THR 255 (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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254A MET* 1.3 79.9 - - - +
256A VAL* 1.3 65.7 + - - +
257A ASP* 3.7 16.6 + - - -
266A GLU 3.6 3.7 + - - -
267A ARG* 3.6 10.2 - - - +
268A PHE 2.9 25.0 + - - -
291A ARG 4.1 9.6 + - - +
293A VAL 3.1 9.6 - - - -
294A ARG* 3.1 39.8 + - - +
295A LEU 4.5 0.2 - - - +
307A LEU* 3.5 23.8 - - + -
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Residues in contact with VAL 256 (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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234A ILE* 3.7 29.4 - - + -
254A MET* 3.9 3.6 - - + -
255A THR* 1.3 79.2 - - - +
257A ASP* 1.3 59.9 + - - +
268A PHE* 3.4 29.6 - - + +
270A LEU* 3.8 14.6 - - + -
292A GLY* 3.1 3.6 - - - -
293A VAL* 3.0 35.0 + - + -
295A LEU* 4.4 7.6 - - + -
375A PHE* 3.7 24.9 - - + -
395A ILE* 4.4 15.5 - - + -
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Residues in contact with ASP 257 (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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255A THR* 3.7 14.3 + - - +
256A VAL* 1.3 73.2 - - - +
258A GLY* 1.3 56.2 + - - +
259A PHE* 3.1 31.5 + - + -
267A ARG* 4.2 7.1 - - - +
268A PHE 3.2 2.9 + - - -
269A CYS* 3.0 34.3 - - - -
270A LEU* 2.8 30.5 + - - +
289A ILE* 3.7 8.5 - - - -
290A GLY 2.9 21.1 - - - +
291A ARG 3.3 15.0 - - - +
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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