Contacts of the strand formed by residues 520 - 525 (chain A) in PDB entry 1UMW
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 ALA 520 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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516A ARG* 3.4 2.1 - - - -
517A THR* 2.8 36.2 + - - +
519A SER* 1.3 80.2 - - - +
521A ILE* 1.3 59.9 - - - +
522A ILE* 3.7 6.1 - - + +
532A ILE* 3.7 24.0 - - + -
533A ASN 3.2 16.2 - - - +
534A PHE* 3.9 10.8 - - + -
535A PHE* 3.4 13.8 - - - -
582A TYR* 4.2 4.9 - - + -
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Residues in contact with ILE 521 (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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414A TRP* 3.7 59.0 - - + +
423A LEU* 4.1 8.5 - - + -
514A TRP* 4.0 22.7 - - + -
515A PHE 3.6 11.2 - - - +
516A ARG* 4.4 5.8 - - + +
520A ALA* 1.3 74.9 - - - +
522A ILE* 1.3 68.5 + - - +
523A LEU* 4.3 17.1 - - + +
531A GLN 3.7 1.0 - - - +
532A ILE* 3.4 4.5 - - - +
533A ASN* 3.1 44.7 + - + +
535A PHE* 3.5 11.8 - - + -
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Residues in contact with ILE 522 (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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514A TRP* 3.1 27.9 - - - +
515A PHE* 2.9 47.8 + - + +
517A THR* 4.2 3.8 - - + -
520A ALA* 3.7 23.8 - - + +
521A ILE* 1.3 80.2 - - - +
523A LEU* 1.3 63.5 + - - +
530A VAL* 4.3 12.1 - - + -
531A GLN 3.4 3.8 - - - +
532A ILE* 4.1 8.5 - - + -
586A MET* 3.6 42.4 - - + -
590A LEU* 4.0 23.1 - - + -
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Residues in contact with LEU 523 (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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411A VAL* 3.8 40.8 - - + -
414A TRP* 4.7 8.3 - - + -
423A LEU* 4.4 8.7 - - + -
425A TYR* 5.8 0.7 - - + -
511A LEU* 4.0 21.1 - - + -
513A THR 4.0 2.0 - - - -
514A TRP* 4.0 18.2 - - + -
521A ILE* 4.3 29.2 - - + -
522A ILE* 1.3 77.4 - - - +
524A HIS* 1.3 61.5 + - - +
525A LEU* 4.0 3.7 + - + +
529A SER 3.9 0.9 - - - +
530A VAL* 3.4 4.3 - - - +
531A GLN* 2.8 60.9 + - + +
533A ASN* 4.9 2.0 - - - +
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Residues in contact with HIS 524 (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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374A LEU* 3.7 42.1 - - + +
511A LEU* 3.5 5.4 - - - +
512A ARG* 2.8 69.6 + - + +
513A THR* 2.9 34.0 + - + +
522A ILE 4.3 0.4 - - - -
523A LEU* 1.3 72.3 - - - +
525A LEU* 1.3 66.0 + - - +
528A GLY* 3.9 14.8 - - - -
529A SER 3.3 11.0 + - - -
530A VAL* 3.7 7.1 - - + +
590A LEU* 4.4 15.0 - - + -
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Residues in contact with LEU 525 (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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409A PHE* 4.7 6.3 - - + +
410A TRP* 4.7 16.4 - - - -
411A VAL* 4.3 17.0 - - + -
425A TYR* 5.2 1.8 - - + -
427A LEU* 4.4 17.9 - - + -
509A PRO* 4.3 18.2 - - + -
510A TYR* 3.5 13.2 - - - +
511A LEU* 4.0 24.7 - - + +
512A ARG* 4.1 1.5 - - - -
523A LEU* 5.1 3.6 - - + +
524A HIS* 1.3 87.8 + - - +
526A SER* 1.3 59.0 + - - +
527A ASN* 3.1 22.7 - - - +
528A GLY* 3.0 18.5 + - - -
529A SER* 2.9 21.7 + - - +
531A GLN* 5.5 4.5 - - + +
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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