Contacts of the strand formed by residues 519 - 523 (chain B) 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 PHE 519 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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479B TYR* 4.7 0.3 - - - -
480B LYS* 3.1 39.5 - - + -
481B TRP 4.0 0.7 - - - -
482B ASN* 3.3 44.0 - - + +
513B TYR* 3.4 46.4 - + - -
514B ASN* 4.0 18.4 - - - +
516B THR* 4.6 1.1 - - - -
517B GLU* 3.2 43.8 + - + -
518B ASN* 1.3 77.2 - - - +
520B VAL* 1.3 62.7 + - - +
521B LEU* 4.1 1.3 - - + -
562B GLY* 3.4 8.0 - - - -
563B LYS* 3.0 25.1 + - - +
621B PHE* 3.7 7.3 - - - -
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Residues in contact with VAL 520 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
245B ILE* 4.6 8.3 - - + -
456B MET* 4.2 14.6 - - + -
479B TYR* 3.9 25.8 - - + -
480B LYS 2.9 7.0 + - - +
481B TRP* 4.0 25.1 - - + +
482B ASN* 2.8 27.0 + - - +
519B PHE* 1.3 77.6 - - - +
521B LEU* 1.3 64.1 + - - +
522B PRO* 2.8 5.7 - - + +
563B LYS* 3.5 20.0 - - + +
564B LYS 4.4 2.5 - - - -
565B LEU* 3.7 29.6 - - + +
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Residues in contact with LEU 521 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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482B ASN* 3.9 21.5 - - + +
485B TRP* 3.9 42.4 - - + -
519B PHE* 4.9 0.9 - - + -
520B VAL* 1.3 71.7 - - - +
522B PRO* 1.3 63.1 - - - +
557B MET* 3.3 36.3 - - + +
560B PHE* 3.5 27.8 - - + +
561B PRO 3.6 17.3 - - - +
562B GLY* 4.1 5.6 - - - +
563B LYS 2.6 19.0 + - - +
564B LYS* 4.5 1.3 - - + +
565B LEU 3.0 25.5 + - - +
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Residues in contact with PRO 522 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
481B TRP* 4.1 41.3 - - + -
482B ASN 3.5 22.7 - - - +
483B LEU* 4.9 5.2 - - + +
485B TRP* 4.5 1.9 - - + -
486B MET* 3.3 21.5 - - + +
520B VAL* 2.8 20.2 - - + +
521B LEU* 1.3 80.3 - - - +
523B LEU* 1.3 74.4 + - - +
524B SER* 3.5 4.4 + - - +
565B LEU* 3.6 19.1 - - + +
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Residues in contact with LEU 523 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
485B TRP* 3.9 12.1 - - + -
486B MET* 4.3 10.5 - - + -
490B LEU* 4.7 2.9 - - + -
522B PRO* 1.3 85.0 - - - +
524B SER* 1.3 64.0 + - - +
527B GLU* 5.2 3.4 - - - -
535B ILE* 4.4 19.3 - - + -
553B TYR* 3.7 29.2 - - + +
554B TYR* 3.7 25.8 - - + -
557B MET* 3.4 25.1 - - - -
565B LEU* 3.1 14.9 + - - +
566B LEU* 3.7 8.5 - - + -
567B PHE* 3.1 21.8 + - - +
570B ASN* 3.3 16.0 - - - +
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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
------------------------------------------------------------
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