Contacts of the strand formed by residues 515 - 523 (chain A) in PDB entry 1NQF
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 ASP 515 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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36A ARG* 2.8 46.6 + - - +
510A GLN* 3.4 32.9 + - + +
513A ASP 3.9 1.4 + - - -
514A PHE* 1.3 72.9 - - - +
516A MSE 1.3 62.3 + - - +
550A ALA 3.9 0.3 - - - +
551A VAL* 3.2 3.6 - - - -
552A ALA* 2.5 55.4 + - + +
554A PRO* 5.8 2.2 - - + -
562A ARG* 5.4 0.2 + - - -
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Residues in contact with MSE 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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36A ARG* 2.8 16.8 + - - -
509A TRP* 2.9 60.2 + - + +
511A LEU* 3.3 38.1 - - + -
514A PHE* 4.2 16.4 - - + +
515A ASP* 1.3 79.7 + - - +
517A GLY* 1.3 58.9 + - - +
549A LEU* 5.7 8.3 - - + -
550A ALA 3.6 4.7 - - - +
551A VAL* 4.1 25.8 - - + -
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Residues in contact with GLY 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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36A ARG* 3.6 11.9 - - - -
506A GLN* 4.3 3.6 - - - -
507A LEU 3.3 9.4 - - - -
508A ASP* 4.0 3.1 - - - -
509A TRP* 4.3 1.3 - - - -
516A MSE 1.3 77.7 - - - +
518A MSE 1.3 61.4 + - - -
519A THR* 4.9 2.8 - - - +
549A LEU* 3.7 6.4 - - - +
550A ALA* 2.9 38.0 + - - +
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Residues in contact with MSE 518 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
505A TYR 3.9 0.7 - - - +
506A GLN* 3.4 3.9 + - - -
507A LEU* 2.8 43.5 + - + +
509A TRP* 4.2 12.6 - - + -
517A GLY* 1.3 72.9 - - - -
519A THR* 1.3 64.3 + - - +
520A MSE 4.6 8.3 - - + -
547A TRP* 2.8 48.0 - - + -
548A ASP 3.5 10.8 - - - +
549A LEU* 3.0 29.2 - - + -
568A LEU* 5.3 4.9 - - + -
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Residues in contact with THR 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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37A TRP* 5.4 2.5 - - + -
47A ARG* 4.0 6.2 + - - -
48A ARG* 3.6 26.7 + - - +
505A TYR 3.4 3.1 - - - -
506A GLN* 2.6 30.7 - - - +
517A GLY 4.9 2.7 - - - +
518A MSE 1.3 79.6 - - - +
520A MSE 1.3 63.9 + - - +
521A GLN* 5.2 2.6 + - - +
547A TRP* 3.3 5.5 - - - +
548A ASP* 2.9 58.1 + - + +
549A LEU* 5.8 0.2 - - - -
550A ALA* 5.9 3.8 - - + +
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Residues in contact with MSE 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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503A VAL* 4.2 23.1 - - + +
504A LYS* 3.6 3.6 - - - +
505A TYR* 2.8 57.2 + - + +
518A MSE 4.6 3.6 - - + -
519A THR* 1.3 77.7 + - - +
521A GLN* 1.3 66.4 + - - +
522A TYR* 4.0 31.6 - - + +
545A SER* 6.1 2.5 - - - -
546A LEU 3.4 4.7 - - - +
547A TRP* 4.0 43.3 - - + +
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Residues in contact with GLN 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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47A ARG* 3.6 62.5 + - - +
48A ARG* 4.1 7.6 - - - +
502A GLN* 4.8 2.0 + - - -
503A VAL 3.4 7.6 - - - +
504A LYS* 3.7 18.0 - - + +
519A THR* 5.2 2.7 + - - +
520A MSE 1.3 80.6 - - - +
522A TYR* 1.3 68.1 + - - +
523A LEU* 3.9 17.0 + - + +
544A VAL 3.8 0.5 - - - +
545A SER* 3.1 4.7 - - - -
546A LEU* 2.8 51.5 + - + +
548A ASP* 5.9 0.2 - - - +
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Residues in contact with TYR 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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501A GLN* 4.8 10.1 - - + -
502A GLN* 3.3 8.7 - - - +
503A VAL* 2.8 49.8 + - + +
520A MSE 4.0 16.2 - - + +
521A GLN* 1.3 75.5 - - - +
523A LEU* 1.3 65.4 + - - +
524A GLY* 3.6 19.8 - - - -
525A THR* 4.7 5.0 - - - +
542A GLY 3.8 13.9 + - - -
543A GLY 4.2 2.2 - - - -
544A VAL* 3.2 27.6 - - - -
545A SER* 3.6 15.0 - - - +
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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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53A ASP* 5.0 3.1 - - + -
499A ALA* 3.5 25.1 - - + -
502A GLN* 3.0 35.2 - - + +
521A GLN* 3.9 16.6 - - + +
522A TYR* 1.3 75.9 - - - +
524A GLY* 1.3 66.8 + - - +
526A ARG* 3.4 33.9 - - - +
543A GLY* 2.9 6.0 - - - -
544A VAL* 2.8 50.5 + - + +
546A LEU* 6.2 3.4 - - + -
575A THR* 5.9 2.7 - - + -
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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