Contacts of the helix formed by residues 478 - 495 (chain A) in PDB entry 2N5T
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 SER 478 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
461A LEU* 4.0 8.6 - - - +
475A GLN* 2.7 35.1 + - - +
476A PRO 3.2 2.4 - - - -
477A MET* 1.3 76.2 - - - +
479A PRO* 1.3 74.5 - - - +
480A SER* 3.1 22.4 + - - -
481A VAL 3.9 3.6 - - - -
482A LEU* 3.0 27.1 + - - +
558A THR* 3.8 3.4 + - - -
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Residues in contact with PRO 479 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
478A SER* 1.3 87.0 - - - +
480A SER* 1.3 56.4 + - - +
482A LEU* 4.7 2.2 - - + -
483A ASN* 2.6 42.3 + - - +
552A ALA 5.4 1.1 - - - +
555A GLN 3.2 27.6 - - - +
556A PRO* 3.6 7.9 - - + +
557A THR* 3.6 20.4 - - - +
558A THR* 3.7 18.4 - - - +
561A LEU* 4.0 15.0 - - + -
397B GLU* 5.4 2.5 - - - +
438B ILE* 3.9 17.7 - - + +
441B HIS* 4.9 1.6 - - + -
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Residues in contact with SER 480 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
460A THR* 4.1 2.8 - - - +
461A LEU* 3.4 19.1 - - - +
478A SER* 3.3 14.1 - - - -
479A PRO* 1.3 79.9 - - - +
481A VAL* 1.3 65.1 + - - +
484A LEU* 3.4 25.1 + - - +
394B ILE 4.5 2.6 + - - -
434B ALA* 3.7 28.5 - - - +
437B THR* 3.4 11.3 - - - +
438B ILE* 3.6 19.2 - - - +
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Residues in contact with VAL 481 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
453A THR* 5.0 1.8 - - + -
456A LEU* 4.5 12.6 - - + -
457A THR* 3.9 34.5 - - - +
460A THR* 4.1 18.2 - - + +
461A LEU* 4.3 4.5 - - + -
475A GLN 4.1 14.1 - - - +
476A PRO* 3.5 24.7 - - + +
478A SER 3.2 2.6 + - - +
480A SER* 1.3 80.5 + - - +
482A LEU* 1.3 60.3 + - - +
484A LEU* 3.2 7.2 + - - +
485A ILE* 2.8 46.6 + - + +
505A LEU* 4.8 1.8 - - + -
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Residues in contact with LEU 482 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
476A PRO 4.3 9.9 - - - +
477A MET* 4.5 9.2 - - + -
478A SER 3.0 16.4 + - - +
479A PRO* 4.4 2.9 - - + +
481A VAL* 1.3 76.1 - - - +
483A ASN* 1.3 65.2 + - - +
485A ILE* 2.9 24.1 + - + +
486A LYS 2.9 19.8 + - - -
505A LEU* 5.1 3.6 - - + -
511A ALA* 5.9 2.5 - - + -
514A LEU* 4.1 22.2 - - + -
515A LEU* 5.3 4.3 - - + -
518A MET* 3.3 20.0 - - - +
552A ALA* 5.2 1.1 - - + -
553A LEU* 3.5 21.8 - - + -
561A LEU* 3.6 40.4 - - + -
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Residues in contact with ASN 483 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
479A PRO* 2.6 34.5 + - - +
482A LEU* 1.3 77.8 - - - +
484A LEU* 1.3 57.1 + - - +
486A LYS* 3.2 9.7 + - - +
487A GLN* 3.0 29.3 + - - +
553A LEU* 3.3 43.5 + - - +
437B THR* 3.9 19.9 + - + +
438B ILE* 5.4 2.0 - - - +
441B HIS* 5.4 3.2 + - - -
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Residues in contact with LEU 484 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
433A PRO* 4.6 10.1 - - + +
436A ALA* 3.9 24.0 - - + +
437A THR* 4.7 9.9 - - - +
456A LEU* 4.4 11.7 - - + -
460A THR* 3.3 34.5 - - + +
480A SER 3.4 16.5 + - - +
481A VAL* 3.2 9.4 + - - +
483A ASN* 1.3 76.1 - - - +
485A ILE* 1.3 61.6 + - - +
487A GLN* 3.3 22.9 + - - +
488A VAL* 3.2 28.4 + - - +
433B PRO* 5.1 1.1 - - + +
437B THR* 3.8 20.0 - - + +
484B LEU* 5.4 5.2 - - + -
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Residues in contact with ILE 485 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
451A ILE* 3.7 27.8 - - + -
453A THR* 4.1 1.8 - - + -
456A LEU* 4.6 2.4 - - + +
481A VAL* 2.8 32.4 + - + +
482A LEU* 3.3 27.6 - - + +
484A LEU* 1.3 70.3 - - - +
486A LYS* 1.3 66.0 + - - +
488A VAL* 3.1 4.6 + - - +
489A ILE* 2.9 41.0 + - + +
501A MET* 3.8 26.0 - - + -
505A LEU* 3.9 17.9 - - + -
515A LEU* 4.6 1.8 - - + -
518A MET* 3.6 16.8 - - + -
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Residues in contact with LYS 486 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
482A LEU 2.9 10.0 + - - +
483A ASN* 3.2 13.4 + - - +
485A ILE* 1.3 74.6 - - - +
487A GLN* 1.3 65.0 + - - +
489A ILE* 3.4 5.0 + - - +
490A ASP* 2.4 70.5 + - - +
518A MET* 3.3 27.7 + - + +
553A LEU* 3.4 29.6 - - + -
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Residues in contact with GLN 487 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
436A ALA 3.6 20.4 - - - +
437A THR* 4.2 9.9 + - - +
439A ALA* 4.4 2.3 - - + +
440A ARG* 5.3 1.6 + - - -
483A ASN 3.0 17.1 + - - +
484A LEU* 3.6 25.5 - - - +
485A ILE 3.1 0.4 - - - -
486A LYS* 1.3 80.7 - - + +
488A VAL* 1.3 57.9 + - - +
490A ASP* 3.6 6.3 + - - +
491A ALA* 3.0 26.7 + - - +
487B GLN* 4.3 18.4 - - - +
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Residues in contact with VAL 488 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
430A VAL* 3.5 45.5 - - + -
436A ALA* 3.8 17.3 - - + +
439A ALA* 4.0 10.3 - - + -
449A PHE* 4.1 9.1 - - + -
451A ILE* 3.9 22.0 - - + -
456A LEU* 5.7 0.7 - - + -
484A LEU 3.2 15.0 + - - +
485A ILE* 3.1 8.0 + - - +
487A GLN* 1.3 75.1 - - - +
489A ILE* 1.3 66.9 + - - +
491A ALA* 3.1 4.3 + - - +
492A SER* 3.0 18.4 + - - -
499A THR* 3.7 10.2 + - + -
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Residues in contact with ILE 489 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
451A ILE* 4.4 0.4 - - + -
485A ILE* 2.9 42.0 + - + +
486A LYS* 3.8 4.0 - - - +
488A VAL* 1.3 72.8 - - - +
490A ASP* 1.3 61.9 + - - +
492A SER* 2.9 26.7 - - - -
493A HIS* 2.8 47.2 + - + +
499A THR* 3.5 24.0 - - + +
515A LEU* 5.7 0.4 - - - -
518A MET* 3.5 38.4 - - + +
519A GLY 3.8 4.9 - - - +
520A LEU* 3.8 23.3 - - + +
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Residues in contact with ASP 490 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
440A ARG* 4.7 12.1 - - - +
486A LYS* 2.4 61.1 + - - +
487A GLN* 3.8 5.9 - - - +
489A ILE* 1.3 79.6 - - - +
491A ALA* 1.3 67.8 + - - +
493A HIS* 3.0 11.7 + - - +
494A ALA* 2.7 26.6 + - - +
518A MET 4.7 3.6 - - - +
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Residues in contact with ALA 491 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
439A ALA* 3.5 42.8 - - + +
440A ARG* 3.8 24.5 - - + +
443A ALA* 3.9 9.1 - - + +
449A PHE* 4.3 2.2 - - + -
487A GLN 3.0 11.1 + - - +
488A VAL 3.3 9.0 - - - +
490A ASP* 1.3 75.9 - - - +
492A SER* 1.3 65.2 + - - +
494A ALA* 3.0 9.7 + - - +
495A GLU* 3.3 8.3 + - - +
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Residues in contact with SER 492 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
443A ALA* 4.6 1.6 - - - -
449A PHE* 3.6 14.7 - - - -
488A VAL 3.0 7.0 + - - -
489A ILE 2.9 12.6 - - - -
491A ALA* 1.3 72.5 - - - +
493A HIS* 1.3 72.3 + - - +
495A GLU* 3.0 9.4 + - - +
497A LYS* 2.8 31.3 + - - +
498A TRP 2.6 37.4 + - - -
499A THR* 2.9 16.0 + - - -
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Residues in contact with HIS 493 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
489A ILE* 2.8 41.9 + - + +
490A ASP* 3.0 13.4 + - - +
492A SER* 1.3 84.3 - - - +
494A ALA* 1.3 67.2 + - - +
496A GLY* 2.9 14.2 + - - +
497A LYS 3.5 10.2 + - - -
499A THR 4.4 0.7 - - - -
518A MET 5.3 0.4 - - - -
519A GLY* 3.2 14.8 + - - -
521A ASP* 3.1 32.9 + - - -
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Residues in contact with ALA 494 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
440A ARG* 4.3 23.8 - - - +
490A ASP 2.7 16.3 + - - +
491A ALA 3.5 5.2 - - - +
493A HIS* 1.3 79.3 - - - +
495A GLU* 1.3 64.8 + - - +
496A GLY 3.5 0.3 + - - -
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Residues in contact with GLU 495 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
440A ARG* 4.8 7.4 - - - +
443A ALA* 3.5 35.0 - - + +
444A LYS* 3.9 33.4 - - - +
491A ALA 3.3 3.0 + - - +
492A SER 3.0 9.4 + - - +
494A ALA* 1.3 81.0 - - - +
496A GLY* 1.3 60.5 + - - +
497A LYS* 3.5 29.3 + - + +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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