Contacts of the strand formed by residues 514 - 523 (chain A) in PDB entry 1NYR
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 VAL 514 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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388A ILE 3.5 0.2 - - - +
389A PHE* 3.3 2.8 - - - -
390A VAL* 2.7 48.5 + - + +
392A PRO* 4.3 17.5 - - + -
395A ILE* 4.1 15.5 - - + -
491A LEU* 4.4 13.5 - - + -
492A ASP 3.5 15.9 - - - +
493A PHE* 3.4 44.2 - - + -
512A ARG 4.7 1.1 - - - +
513A PRO* 1.3 78.1 - - - +
515A VAL* 1.3 66.2 + - - +
516A ILE* 5.5 0.2 - - + -
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Residues in contact with VAL 515 (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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340A MET* 3.7 20.4 - - + -
387A HIS* 4.2 18.6 - - + -
388A ILE 3.1 7.2 - - - +
389A PHE* 3.7 15.5 - - + -
490A GLN 3.4 0.3 - - - +
491A LEU* 3.8 1.4 - - - -
492A ASP* 2.7 53.3 + - + +
496A PRO* 3.4 26.5 - - + -
514A VAL* 1.3 76.4 - - - +
516A ILE* 1.3 71.8 + - - +
517A HIS* 3.8 21.5 - - + +
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Residues in contact with ILE 516 (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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386A SER 3.6 1.4 - - - +
387A HIS* 3.6 2.3 - - - -
388A ILE* 2.8 39.1 + - + +
390A VAL* 4.2 18.4 - - + -
395A ILE* 4.0 19.7 - - + +
398A GLU* 3.8 30.1 - - + -
399A PHE* 4.0 28.5 - - + +
402A VAL* 4.6 12.3 - - + -
489A ALA* 4.8 0.4 - - + -
490A GLN 3.0 15.3 - - - +
491A LEU* 4.6 9.9 - - + -
514A VAL* 5.5 0.2 - - + -
515A VAL* 1.3 79.0 - - - +
517A HIS* 1.3 67.2 + - - +
518A ARG* 4.7 6.3 - - + -
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Residues in contact with HIS 517 (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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336A CYS* 3.2 24.9 - - + -
340A MET* 5.9 0.2 - - + -
386A SER 3.6 6.1 - - - -
387A HIS* 2.8 8.1 + + - -
468A TYR* 3.7 20.4 + + - -
489A ALA* 3.3 0.3 - - - -
490A GLN* 2.6 59.2 + - + +
492A ASP* 3.1 43.7 + - + +
495A LEU* 4.5 2.4 - - + +
515A VAL* 3.8 8.8 - - + +
516A ILE* 1.3 74.5 - - - +
518A ARG* 1.3 61.0 + - - +
1001A ZN 1.8 34.3 - - - -
1004A THR* 3.0 10.3 - - + +
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Residues in contact with ARG 518 (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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285A GLU* 2.5 30.7 + - - -
290A TYR* 3.2 31.0 + - - -
384A ASN* 3.4 29.8 + - - +
385A ASP* 3.5 4.8 - - - +
386A SER* 3.1 50.2 + - - +
388A ILE* 4.4 12.8 - - + -
402A VAL* 3.5 31.3 - - + +
405A MET* 3.6 7.3 - - - +
406A ILE* 5.7 0.4 - - + -
488A THR 2.8 14.1 - - - +
489A ALA* 3.9 2.9 - - + -
516A ILE* 4.7 3.6 - - + +
517A HIS* 1.3 78.4 - - - +
519A GLY* 1.3 57.4 + - - +
520A VAL* 3.4 23.4 - - - +
1004A THR* 3.8 9.1 - - - +
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Residues in contact with GLY 519 (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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383A LEU* 4.8 14.1 - - - -
384A ASN 3.3 13.0 - - - -
406A ILE* 4.4 1.5 - - - +
486A LEU 4.3 0.3 - - - +
487A SER* 3.0 30.0 - - - -
488A THR* 2.8 20.4 + - - +
518A ARG* 1.3 73.7 - - - +
520A VAL* 1.3 60.5 + - - -
522A SER* 4.1 5.2 + - - -
1003A ATP 6.1 0.4 - - - -
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Residues in contact with VAL 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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281A ILE* 4.3 5.2 - - + -
285A GLU* 4.8 0.2 - - - +
384A ASN* 3.1 12.0 - - - +
402A VAL* 5.3 1.8 - - + -
405A MET* 3.6 16.6 - - + -
406A ILE* 4.0 30.1 - - + +
409A VAL* 3.6 37.5 - - + -
410A TYR* 4.2 5.4 + - + -
487A SER* 2.7 24.6 + - - -
518A ARG* 3.4 34.5 - - - +
519A GLY* 1.3 68.7 - - - +
521A VAL* 1.3 62.5 + - - +
522A SER 3.0 7.3 + - - -
527A PHE* 4.6 0.7 - - - -
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Residues in contact with VAL 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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277A ILE* 4.1 23.3 - - + -
280A TYR* 5.1 0.7 - - + -
281A ILE* 4.2 20.2 - - + -
384A ASN* 2.9 30.3 - - + +
409A VAL* 4.2 14.1 - - + -
413A PHE* 4.2 4.0 - - + -
520A VAL* 1.3 75.3 - - + +
522A SER* 1.3 62.6 + - - +
523A THR 3.9 1.4 - - - +
524A MET* 4.6 7.1 - - - +
527A PHE* 3.0 63.6 - - + +
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Residues in contact with SER 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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383A LEU* 3.3 12.8 - - - +
384A ASN* 2.8 35.9 + - - +
486A LEU* 2.9 28.1 + - - -
519A GLY 4.5 4.0 - - - -
520A VAL 3.0 8.3 + - - +
521A VAL* 1.3 81.5 - - - +
523A THR* 1.3 70.0 + - - -
524A MET* 4.2 0.3 + - - +
526A ARG* 3.8 11.3 - - - +
527A PHE* 4.0 10.8 - - - -
1003A ATP 2.7 21.9 + - - -
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Residues in contact with THR 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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381A MET* 3.3 31.4 - - - +
382A THR 3.3 13.0 + - - -
383A LEU* 3.7 7.5 + - - +
521A VAL 4.3 0.9 - - - -
522A SER* 1.3 82.0 + - - +
524A MET* 1.3 62.8 + - - +
525A GLU* 3.6 6.3 - - + +
526A ARG* 3.0 29.6 - - + +
527A PHE* 2.9 23.7 + - - +
1003A ATP 3.1 36.5 + - + +
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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