Contacts of the strand formed by residues 563 - 567 (chain A) in PDB entry 1M7X
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 563 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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239A PHE 2.9 26.8 + - - -
241A ALA 2.6 23.8 + - - -
243A ILE* 3.5 37.7 - - + +
479A TYR* 3.9 20.9 - - + -
519A PHE 3.2 14.2 + - - +
520A VAL* 4.2 11.4 - - + -
521A LEU* 2.9 24.4 + - - +
562A GLY* 1.3 78.5 - - - +
564A LYS* 1.3 65.0 + - - +
610A TYR* 3.7 11.2 + - - +
617A HIS 3.1 16.6 + - - -
620A ASP* 3.1 16.4 + - - +
621A PHE* 3.9 12.3 - - + -
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Residues in contact with LYS 564 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
243A ILE 2.9 11.8 + - - +
244A SER* 3.4 13.7 - - - +
245A ILE* 2.7 35.2 + - - +
520A VAL* 4.4 2.2 - - - -
521A LEU* 3.8 5.6 - - + +
557A MET* 2.9 33.6 + - + +
558A TRP* 3.2 45.9 + - + +
560A PHE 2.9 20.6 + - - -
562A GLY 2.6 21.6 + - - +
563A LYS* 1.3 76.3 - - - +
565A LEU* 1.3 58.4 + - - +
610A TYR* 3.4 36.6 - - + -
616A MET 4.9 0.9 - - - -
643A ARG* 4.9 1.0 - - - +
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Residues in contact with LEU 565 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
245A ILE* 3.4 24.0 - - + +
247A GLU* 3.8 26.7 - - + +
285A GLU* 3.6 22.7 - - - +
481A TRP* 3.4 32.8 - - + +
520A VAL* 3.8 14.1 - - + -
521A LEU 3.1 8.7 + - - +
522A PRO* 4.1 8.1 - - + -
523A LEU 3.2 21.6 + - - +
524A SER* 4.0 14.4 - - - -
557A MET* 3.3 12.0 - - - +
564A LYS* 1.3 77.3 - - - +
566A LEU* 1.3 68.5 + - - +
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Residues in contact with LEU 566 (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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245A ILE 2.8 14.0 + - - +
246A TYR* 3.5 8.2 - - + -
247A GLU 3.0 18.7 + - - -
281A PHE* 4.2 15.7 - - + -
523A LEU* 3.6 31.0 - - + -
554A TYR* 4.2 10.8 - - + +
557A MET* 4.6 1.1 - - + -
558A TRP* 4.2 27.1 - - + -
565A LEU* 1.3 77.9 - - - +
567A PHE* 1.3 66.1 + - - +
570A ASN* 3.6 17.7 - - + -
571A GLU* 3.6 39.0 - - + +
603A VAL* 4.4 5.6 - - + -
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Residues in contact with PHE 567 (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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246A TYR* 4.6 0.9 - - - -
247A GLU* 2.9 51.7 - - + +
248A VAL* 4.0 2.9 - - - -
249A HIS* 4.0 0.9 - - + -
287A LEU* 3.9 17.5 - - + -
523A LEU 2.9 17.7 + - - +
524A SER 3.7 1.3 - - - -
525A HIS* 3.5 35.9 - - + +
528A VAL* 4.3 9.4 - - + -
565A LEU* 4.3 0.4 - - - +
566A LEU* 1.3 75.5 - - - +
568A MET* 1.3 97.2 + - + +
569A GLY 3.4 0.2 + - - -
570A ASN* 3.2 27.8 + - - +
571A GLU* 4.0 1.9 - - - +
578A TRP* 3.4 48.7 - + + -
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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