Contacts of the strand formed by residues 519 - 522 (chain A) in PDB entry 1HMW
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 TRP 519 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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498A ILE* 3.4 37.2 - - + -
499A SER* 3.2 42.5 - - - -
500A THR* 3.3 13.7 + - - +
501A ALA 5.3 0.4 - - - -
517A GLN 3.8 13.0 - - - -
518A PHE* 1.3 86.2 - - - +
520A LEU* 1.3 66.1 + - - +
521A LEU* 4.2 5.4 - - + -
527A TYR 3.2 11.0 - - - +
528A TYR* 4.2 14.8 - + + -
583A LEU* 6.5 0.2 - - + -
589A PRO* 4.9 11.0 - - + -
592A ILE* 3.3 49.6 - - + -
593A LYS* 4.1 35.2 + - + +
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Residues in contact with LEU 520 (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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497A VAL* 3.8 18.4 - - + -
498A ILE 3.2 7.9 - - - +
499A SER* 3.2 30.7 - - - -
504A THR* 6.1 0.2 - - - +
512A PHE* 5.5 3.1 - - + -
518A PHE* 3.8 16.8 - - + -
519A TRP* 1.3 79.5 - - - +
521A LEU* 1.3 59.6 + - - +
526A GLY* 3.2 3.5 - - - -
527A TYR* 2.8 45.9 + - + +
529A PHE* 4.9 2.0 - - + -
535A LEU* 4.8 4.9 - - + -
537A LEU* 4.6 18.6 - - + -
563A PHE* 5.3 1.8 - - + -
565A LEU* 3.7 37.5 - - + -
592A ILE* 4.3 1.4 - - - +
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Residues in contact with LEU 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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496A PRO 3.8 2.1 - - - +
497A VAL* 3.5 3.7 - - - +
498A ILE* 2.8 45.6 + - + +
519A TRP* 4.2 2.9 - - + -
520A LEU* 1.3 76.4 - - - +
522A HIS* 1.3 67.3 + - - +
524A ALA* 4.0 4.9 - - - +
525A ILE 3.3 30.7 - - - +
526A GLY* 3.9 3.1 - - - +
586A ILE* 3.7 42.4 - - + +
587A ASN 5.7 0.4 - - - -
588A LYS 4.7 1.6 - - - +
589A PRO* 4.3 23.8 - - + -
592A ILE* 3.7 16.6 - - + -
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Residues in contact with HIS 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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491A SER* 4.4 4.2 + - - -
492A TRP 3.5 16.2 - - - -
493A LEU* 3.3 20.9 - - + +
494A ASN 3.1 21.2 + - - -
495A GLY 4.0 9.4 - - - -
496A PRO 4.3 4.9 - - - -
497A VAL* 3.7 14.8 - - + -
521A LEU* 1.3 78.3 - - - +
523A ASP* 1.3 80.6 + - + +
524A ALA 3.1 1.8 - - - -
525A ILE* 2.7 39.1 + - - +
527A TYR* 4.8 1.5 + - + -
563A PHE* 3.5 56.8 - + + -
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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