Contacts of the strand formed by residues 523 - 531 (chain A) in PDB entry 1NA8
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 523 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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518A TYR* 3.3 12.9 - + + -
519A ASP* 3.3 3.1 - - - -
520A GLN 2.7 34.1 + - - +
521A HIS* 3.2 2.6 - - + +
522A GLY* 1.3 78.9 - - - +
524A ARG* 1.3 60.4 + - - +
525A ILE* 3.9 15.7 - - + -
547A MET* 4.1 10.3 - - + -
548A LEU 3.3 14.1 - - - -
549A SER* 4.5 0.4 - - - +
555A ILE* 3.6 21.8 - - + -
558A ILE* 3.8 25.8 - - + -
580A LEU* 3.5 24.5 - - + -
612A LEU* 3.9 17.0 - - + -
614A PHE* 3.8 48.5 - + + -
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Residues in contact with ARG 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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516A THR* 4.9 10.0 + - + +
518A TYR 3.1 10.5 - - - +
519A ASP* 3.4 22.1 + - + +
522A GLY 5.0 3.8 - - - +
523A PHE* 1.3 73.9 - - - +
525A ILE* 1.3 70.3 + - - +
526A LEU* 4.5 13.1 - - + +
546A SER 3.7 0.7 - - - +
547A MET* 3.4 4.7 - - - -
548A LEU* 2.9 57.3 + - + +
550A THR* 6.4 1.8 - - - -
519B ASP* 5.0 1.2 + - - -
522B GLY* 5.5 4.0 + - - -
524B ARG* 2.9 55.9 - - - +
548B LEU* 5.6 9.3 - - - +
550B THR* 3.8 33.4 + - - +
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Residues in contact with ILE 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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516A THR* 3.7 2.6 - - - -
517A VAL* 2.9 34.2 + - + -
518A TYR* 2.9 30.9 + - + +
523A PHE* 3.9 12.6 - - + -
524A ARG* 1.3 77.1 - - - +
526A LEU* 1.3 64.8 + - - +
527A PHE* 4.5 1.3 - - + -
545A VAL* 3.6 23.3 - - + -
546A SER 3.4 1.1 - - - -
547A MET* 3.5 41.1 - - + -
560A PHE* 4.1 19.1 - - + -
612A LEU* 4.1 21.1 - - + -
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Residues in contact with LEU 526 (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 PRO* 4.7 7.4 - - + -
515A VAL 3.4 5.2 - - - +
516A THR* 3.5 30.1 - - + +
524A ARG* 4.5 16.8 - - + +
525A ILE* 1.3 78.6 - - - +
527A PHE* 1.3 69.8 + - - +
528A HIS* 4.2 21.8 - - + +
544A VAL 3.6 0.5 - - - +
545A VAL* 3.3 7.1 - - - +
546A SER* 2.8 41.6 + - - +
548A LEU* 4.0 25.6 - - + -
550B THR* 4.1 20.4 - - + -
583B PHE* 4.3 9.0 - - + -
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Residues in contact with PHE 527 (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 PRO* 3.1 5.5 - - - +
515A VAL* 2.9 37.9 + - + +
517A VAL* 3.6 25.1 - - + -
525A ILE* 4.5 1.3 - - + -
526A LEU* 1.3 80.6 - - - +
528A HIS* 1.3 63.5 + - - +
529A PHE* 4.1 17.2 - + + -
543A VAL* 3.7 19.7 - - + -
544A VAL 3.8 2.0 - - - -
545A VAL* 3.5 29.6 - - + -
560A PHE* 3.6 31.6 - + - -
562A SER* 4.8 0.2 - - - -
596A LEU* 5.1 2.0 - - + -
608A LEU* 4.4 15.3 - - + -
627A VAL* 4.2 14.6 - - + -
630A PHE* 4.1 26.5 - + - -
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Residues in contact with HIS 528 (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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509A PRO* 4.7 7.6 - - + -
510A SER 4.8 7.0 - - - +
512A ILE 4.8 7.4 - - - -
514A PRO* 3.4 40.1 - - + +
526A LEU* 4.2 11.4 - - + +
527A PHE* 1.3 74.6 - - - +
529A PHE* 1.3 65.6 + - - +
543A VAL* 3.4 5.9 - - - +
544A VAL* 2.8 44.2 + - + +
546A SER* 4.7 1.4 + - - -
550B THR 4.6 2.2 + - - -
551B ALA 6.3 0.2 - - - -
552B PRO* 6.2 3.1 - - + +
583B PHE* 3.4 44.7 + + - +
585B PRO* 4.0 28.4 - - + +
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Residues in contact with PHE 529 (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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509A PRO* 3.6 3.1 - - - +
510A SER* 2.8 31.1 + - - +
512A ILE* 3.6 31.0 + - + +
513A LEU 4.2 8.3 - - - -
515A VAL* 3.6 26.2 - - + -
527A PHE* 4.1 22.4 - + + -
528A HIS* 1.3 76.4 - - - +
530A ALA* 1.3 62.4 + - - +
541A LEU* 4.0 10.1 - - + -
542A VAL 3.6 2.2 - - - -
543A VAL* 4.0 19.1 - - + -
544A VAL* 6.2 0.2 - - - -
627A VAL* 6.0 0.7 - - + -
629A GLN 3.6 20.9 - - - -
630A PHE* 3.6 28.7 - + - -
631A PRO* 3.7 24.5 - - + -
639A LEU* 5.0 2.5 - - + -
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Residues in contact with ALA 530 (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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507A ILE* 3.5 26.9 - - + -
508A LYS 3.5 19.7 - - - +
509A PRO* 3.7 3.4 - - + -
510A SER 4.1 5.2 - - - +
529A PHE* 1.3 77.2 - - - +
531A ARG* 1.3 64.9 + - - +
532A ASP 3.8 0.2 + - - -
541A LEU* 3.7 7.8 - - - +
542A VAL* 3.1 35.8 + - + +
544A VAL* 5.5 1.3 - - + -
639A LEU* 3.9 10.0 - - - +
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Residues in contact with ARG 531 (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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507A ILE* 5.0 1.7 - - - +
508A LYS 4.5 6.3 + - - +
530A ALA* 1.3 83.9 - - - +
532A ASP* 1.3 77.9 + - - +
533A PRO* 3.2 13.9 - - + +
540A VAL 5.0 0.7 - - - -
542A VAL* 3.9 3.0 - - - +
636A TRP 3.8 20.2 - - - +
637A GLY* 3.3 18.0 + - - +
638A SER* 2.9 36.8 + - - +
639A LEU* 3.2 25.0 + - + +
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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
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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