Contacts of the strand formed by residues 538 - 543 (chain A) in PDB entry 4HXG
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 LEU 538 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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472A THR* 4.4 3.6 - - + -
473A ASN* 4.2 2.5 - - - +
476A LEU* 3.9 20.2 - - + -
485A GLY* 3.2 25.1 - - - +
487A SER* 4.1 13.9 - - - +
534A VAL* 5.4 3.6 - - + -
536A ALA 4.0 7.9 - - - +
537A PRO* 1.3 74.7 - - - +
539A LEU* 1.3 72.0 + - - +
540A LEU* 4.1 14.1 - - + -
557A PHE* 3.9 28.7 - - + -
561A LEU* 3.9 16.2 - - + -
567A GLU 3.2 6.8 + - - +
568A VAL* 3.2 11.9 - - + +
569A TYR* 2.9 27.9 + - - -
599A PHE* 3.8 3.8 - - - -
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Residues in contact with LEU 539 (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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485A GLY 3.1 6.9 + - - -
486A ILE* 3.4 12.7 - - + +
487A SER 3.0 26.3 + - - +
538A LEU* 1.3 74.4 - - - +
540A LEU* 1.3 83.2 + - - +
541A ILE* 3.9 23.1 - - + -
569A TYR* 3.5 18.8 - - + +
570A ILE 4.7 0.2 - - - -
571A ALA* 4.4 10.1 - - + +
595A LEU* 4.1 24.2 - - + +
599A PHE* 3.6 48.3 - - + -
611A PHE* 5.5 2.0 - - + -
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Residues in contact with LEU 540 (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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473A ASN* 4.2 6.3 - - - +
487A SER* 3.6 28.9 - - - +
538A LEU* 4.0 16.1 - - + -
539A LEU* 1.3 81.1 - - - +
541A ILE* 1.3 60.8 + - - +
554A SER* 3.3 39.0 - - - +
557A PHE* 4.3 9.6 - - + -
558A TYR* 3.5 28.3 - - + +
568A VAL* 3.9 12.8 - - + -
569A TYR 2.7 13.2 + - - +
570A ILE* 3.3 12.9 - - + -
571A ALA 2.9 25.3 + - - -
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Residues in contact with ILE 541 (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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486A ILE* 3.8 14.1 - - + -
487A SER 2.9 13.3 + - - +
488A GLU* 3.5 34.0 - - + +
489A ASN* 3.1 24.1 + - - -
539A LEU* 3.9 22.7 - - + -
540A LEU* 1.3 79.8 - - - +
542A HIS* 1.3 68.7 + - - +
554A SER* 3.7 4.8 + - - -
570A ILE* 5.5 0.4 - - - -
571A ALA* 3.5 11.7 - - + +
573A PHE* 4.1 21.8 - - + -
580A HIS* 4.4 10.5 - - + +
592A ARG* 4.5 14.8 - - + +
595A LEU* 4.7 7.4 - - + -
596A PHE* 5.1 6.7 - - + -
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Residues in contact with HIS 542 (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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489A ASN* 3.6 29.0 - - - -
490A GLY 4.6 0.2 - - - -
541A ILE* 1.3 74.4 - - - +
543A SER* 1.3 80.9 + - - +
546A ASP* 4.2 3.2 + - - +
549A CYS 2.7 29.7 + - - -
550A PRO 3.3 10.9 - - - -
551A LEU* 3.2 41.2 + - + -
553A GLN* 4.6 1.8 - - + -
554A SER* 2.4 33.7 + - - +
570A ILE* 5.3 0.7 - - + -
571A ALA 3.0 9.1 + - - +
572A ILE* 3.5 6.9 - - + -
573A PHE* 2.7 36.3 + - - +
580A HIS* 4.4 3.8 - - - -
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Residues in contact with SER 543 (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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489A ASN* 3.3 7.4 + - - +
542A HIS* 1.3 97.0 - - - +
544A LEU* 1.3 65.2 + - - +
545A GLU 3.3 0.9 + - - -
546A ASP* 3.5 8.7 + - - +
551A LEU* 5.0 1.6 + - - +
572A ILE* 5.1 0.9 - - - -
573A PHE* 3.5 6.7 - - - +
575A LYS 3.9 8.1 - - - -
576A GLY 3.0 24.3 + - - -
577A ALA 3.1 17.8 + - - -
580A HIS* 3.2 24.8 - - - -
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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