Contacts of the strand formed by residues 456 - 460 (chain A) in PDB entry 5MKE
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 GLN 456 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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379A HIS* 4.3 7.6 - - + -
438A VAL* 3.8 2.4 - - + +
440A ARG* 2.5 74.6 + - + +
441A LEU* 4.3 0.2 - - - +
442A LEU* 6.3 0.9 - - + -
455A TRP* 1.3 78.0 - - - +
457A PHE* 1.3 88.9 + - - +
458A GLN* 5.6 0.5 - - - +
556A ILE* 5.5 11.1 - - + +
1007A PX6 2.6 32.6 + - - -
652B ALA 3.5 4.3 + - - +
653B ASN* 2.4 34.3 + - - +
654B ARG* 4.4 8.9 - - - +
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Residues in contact with PHE 457 (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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250A THR* 5.7 4.3 - - + -
253A MET 5.4 0.7 - - - -
254A SER* 3.7 23.8 - - - -
257A PHE* 5.3 11.7 - + + -
258A LEU* 4.6 14.1 - - + -
437A CYS* 5.1 8.7 - - - -
438A VAL* 3.4 12.8 - - - +
439A VAL* 4.0 29.8 - - + -
441A LEU* 5.2 6.7 - - + -
455A TRP* 4.5 15.8 - + + -
456A GLN* 1.3 101.1 + - - +
458A GLN* 1.3 67.0 + - - +
459A PRO* 4.5 2.5 - - + +
621B THR* 4.7 10.4 - - - +
622B GLN* 3.3 38.4 - - + +
652B ALA 5.4 0.2 + - - -
653B ASN* 4.9 1.9 + - - +
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Residues in contact with GLN 458 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
437A CYS* 3.0 4.9 - - - -
438A VAL* 2.7 55.1 + - + +
456A GLN* 5.6 1.0 - - - +
457A PHE* 1.3 77.9 - - - +
459A PRO* 1.3 90.9 + - - +
552A ALA* 6.0 0.9 - - + -
555A GLN* 4.7 3.6 - - + -
556A ILE* 3.2 54.5 - - + +
559A ASN* 2.9 32.5 - - - +
560A ASN* 4.9 3.1 + - - -
621B THR* 4.3 11.1 - - - +
653B ASN* 4.5 7.6 + - - +
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Residues in contact with PRO 459 (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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242A MET* 5.6 8.6 - - + +
246A VAL* 4.7 15.9 - - + -
249A TYR* 5.4 2.5 - - + -
250A THR* 5.2 12.1 - - + -
435A LEU* 3.8 19.1 - - + -
436A PHE 3.1 5.4 - - - +
437A CYS* 3.8 10.1 - - - -
457A PHE 4.5 2.2 - - - +
458A GLN* 1.3 119.4 + - - +
460A LEU* 1.3 64.1 + - - +
555A GLN* 4.0 8.5 - - - +
559A ASN* 4.9 5.8 + - - +
620B GLY 5.6 1.6 - - - +
621B THR* 4.7 15.0 - - + +
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Residues in contact with LEU 460 (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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242A MET* 5.2 2.5 - - - -
435A LEU* 3.0 9.9 - - - +
436A PHE* 2.1 82.5 + - + +
437A CYS* 4.3 0.9 - - - +
438A VAL* 5.3 3.8 - - + -
458A GLN 5.1 0.4 - - - +
459A PRO* 1.3 73.5 - - - +
461A LYS* 1.3 74.1 + - - +
462A LEU* 3.5 16.6 - - + +
548A PHE* 3.4 38.6 - - + -
552A ALA* 6.0 0.7 - - + -
555A GLN* 3.1 44.0 - - + +
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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