Contacts of the helix formed by residues 516 - 533 (chain B) in PDB entry 3HN3
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 516 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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505B TYR* 5.4 0.9 - - + -
506B SER 6.1 1.1 - - - +
510B ASP* 3.7 14.1 - - + -
513B HIS* 3.1 31.7 + - + +
515B GLU* 1.3 84.2 - - + +
517B ILE* 1.3 64.4 + - - +
518B GLN 3.4 1.8 - - - -
519B LEU* 3.3 8.1 + - + +
520B GLN* 3.0 40.2 + - - +
194D LYS 3.9 8.1 - - - +
195D TYR* 3.6 28.3 - - + -
196D PRO* 3.3 35.0 - - + -
199D TYR* 3.8 16.4 - - + +
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Residues in contact with ILE 517 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
505B TYR* 3.7 27.4 - - + +
506B SER* 3.7 22.4 - - - +
514B LEU* 3.4 24.9 + - + +
515B GLU 3.4 0.2 - - - -
516B LEU* 1.3 78.3 - - - +
518B GLN* 1.3 58.9 + - - +
520B GLN* 3.3 0.9 + - - +
521B LEU* 2.9 32.3 + - + +
565B LEU* 4.0 24.2 - - + +
568B GLN* 3.8 19.3 - - + +
569B TYR* 3.6 43.7 - - + +
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Residues in contact with GLN 518 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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514B LEU 5.0 0.8 + - - -
515B GLU 4.8 3.6 + - - +
516B LEU 3.4 0.8 - - - -
517B ILE* 1.3 77.5 - - - +
519B LEU* 1.3 62.6 + - - +
521B LEU* 3.9 5.0 - - - +
522B ALA* 3.0 25.6 + - - +
568B GLN* 2.9 41.7 + - - +
571B LEU* 3.7 33.7 - - + +
572B GLY* 4.6 9.0 + - - +
575B GLN* 5.7 3.1 - - - +
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Residues in contact with LEU 519 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
515B GLU 5.2 2.1 + - - +
516B LEU* 3.3 12.2 + - + +
517B ILE 3.3 0.4 - - - -
518B GLN* 1.3 77.6 - - - +
520B GLN* 1.3 64.1 + - - +
522B ALA* 3.2 8.1 + - + +
523B THR* 3.1 30.4 + - - +
192D THR 3.7 15.5 - - - +
193D SER* 3.5 15.9 - - - +
194D LYS 3.5 3.8 - - - +
195D TYR* 3.4 42.4 - - - +
196D PRO* 3.9 8.7 - - + -
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Residues in contact with GLN 520 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
505B TYR* 3.1 49.8 + - + +
506B SER 4.9 0.7 + - - -
509B HIS* 4.8 0.9 + - - -
510B ASP* 3.2 25.7 + - - +
516B LEU* 3.0 30.9 + - - +
517B ILE 4.0 0.2 - - - +
519B LEU* 1.3 75.8 - - - +
521B LEU* 1.3 56.6 + - - +
523B THR* 3.5 2.9 + - - -
524B GLN* 3.0 27.4 + - - +
193D SER 4.4 4.7 - - - -
194D LYS* 2.9 55.3 + - + +
195D TYR* 4.0 3.6 - - - -
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Residues in contact with LEU 521 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
505B TYR* 3.9 7.5 - - + -
517B ILE* 2.9 18.6 + - + +
518B GLN* 3.9 4.5 - - - +
520B GLN* 1.3 73.8 - - - +
522B ALA* 1.3 65.5 + - - +
524B GLN* 3.1 20.1 + - - +
525B PHE* 3.0 42.1 + - + -
538B GLN* 3.6 24.5 - - - +
568B GLN 4.7 1.1 - - - +
569B TYR* 3.5 59.0 - - + +
572B GLY* 3.8 15.9 - - - -
573B LEU* 4.0 5.4 - - + +
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Residues in contact with ALA 522 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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518B GLN 3.0 18.8 + - - +
519B LEU* 3.2 9.4 + - + +
521B LEU* 1.3 77.7 - - - +
523B THR* 1.3 57.1 + - - +
525B PHE* 3.5 2.6 + - - +
526B GLU* 3.0 44.5 + - - +
572B GLY* 6.0 0.6 - - - -
576B LYS* 4.0 23.3 - - - +
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Residues in contact with THR 523 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
519B LEU* 3.1 14.6 + - - +
520B GLN* 3.8 5.4 - - - +
522B ALA* 1.3 75.4 - - - +
524B GLN* 1.3 60.2 + - - +
526B GLU* 3.7 11.2 + - - +
527B ASN* 2.9 57.8 + - - +
193D SER* 2.6 49.6 + - - +
194D LYS* 5.1 10.8 - - + +
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Residues in contact with GLN 524 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2B MPD 3.1 22.7 - - + +
501B LEU* 3.7 12.5 - - + +
503B SER* 2.9 17.1 + - - -
505B TYR* 2.6 28.1 + - - +
520B GLN 3.0 15.5 + - - +
521B LEU* 3.2 12.6 - - - +
523B THR* 1.3 77.2 - - - +
525B PHE* 1.3 80.9 + - - +
527B ASN* 3.8 2.4 - - - +
528B TRP* 3.1 41.0 + - + -
538B GLN* 2.7 28.9 + - - -
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Residues in contact with PHE 525 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
501B LEU* 4.8 0.2 - - + -
521B LEU* 3.0 41.8 + - + +
522B ALA* 4.0 3.4 - - - +
524B GLN* 1.3 94.8 - - + +
526B GLU* 1.3 57.6 + - - +
528B TRP* 4.9 0.2 - - - -
529B TYR* 2.9 27.9 + - - +
536B ILE* 3.8 28.3 - - + +
538B GLN* 3.6 20.0 - - + -
572B GLY 4.4 6.1 - - - -
573B LEU* 3.7 26.2 - - + -
576B LYS* 3.6 25.6 - - + -
580B TYR* 3.3 22.2 + - + +
581B VAL* 3.6 25.4 - - + -
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Residues in contact with GLU 526 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
522B ALA* 3.0 38.7 + - - +
523B THR* 3.7 10.7 + - - +
525B PHE* 1.3 75.8 - - - +
527B ASN* 1.3 66.1 + - - +
529B TYR* 4.4 0.8 - - - +
530B LYS* 3.0 27.9 + - - +
576B LYS* 4.4 16.2 + - - -
580B TYR* 4.0 6.1 - - - +
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Residues in contact with ASN 527 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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487B TYR* 3.4 49.4 + - + -
523B THR* 2.9 42.3 + - - +
524B GLN* 3.8 4.4 - - - +
526B GLU* 1.3 80.8 - - - +
528B TRP* 1.3 62.8 + - + +
530B LYS* 3.6 4.0 + - - +
531B LYS* 3.3 23.2 + - - +
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Residues in contact with TRP 528 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2B MPD 3.3 22.0 + - + +
483B SER* 4.2 3.4 - - - -
485B SER 3.3 22.9 - - - -
487B TYR* 3.4 33.0 - + + +
490B ASP* 3.5 25.1 - - + -
493B ALA* 4.0 23.1 - - + -
499B ILE* 3.7 20.2 - - + +
501B LEU* 3.4 35.7 - - + -
524B GLN* 3.1 31.2 + - + +
527B ASN* 1.3 78.6 - - + +
529B TYR* 1.3 63.5 + - - +
531B LYS* 3.3 3.2 + - - +
532B TYR* 3.0 44.0 + + - +
536B ILE* 4.0 17.7 - - + -
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Residues in contact with TYR 529 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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333B LYS* 2.7 35.0 + - - +
334B SER* 3.9 8.0 - - - -
499B ILE* 6.1 0.4 - - - -
525B PHE 2.9 19.6 + - - +
526B GLU* 4.4 1.1 - - - +
528B TRP* 1.3 75.1 - - - +
530B LYS* 1.3 68.0 + - - +
533B GLN* 2.9 35.2 + - + +
534B LYS 3.2 34.5 - - - -
536B ILE* 4.1 4.4 - - + +
580B TYR* 3.5 56.1 - + + -
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Residues in contact with LYS 530 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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526B GLU 3.0 19.8 + - - +
527B ASN* 4.0 4.5 - - - +
529B TYR* 1.3 80.4 - - - +
531B LYS* 1.3 63.4 + - - +
533B GLN* 3.9 15.9 + - - +
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Residues in contact with LYS 531 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
487B TYR* 3.5 41.3 - - + +
488B ALA* 4.0 19.7 - - - +
527B ASN 3.3 14.3 + - - +
528B TRP 3.9 2.9 - - - +
529B TYR 3.2 0.4 - - - -
530B LYS* 1.3 83.4 - - - +
532B TYR* 1.3 90.3 + - + +
533B GLN* 4.6 3.9 + - - +
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Residues in contact with TYR 532 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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487B TYR 3.7 11.3 + - - -
488B ALA 5.7 0.5 + - - -
490B ASP 3.3 19.2 + - - -
493B ALA* 3.5 22.9 - - + -
494B PRO* 3.6 40.0 - - + +
499B ILE* 3.3 25.1 - - + -
528B TRP* 3.0 23.9 + + - +
531B LYS* 1.3 120.2 + - + +
533B GLN* 1.3 73.5 + - - +
534B LYS* 3.1 20.1 - - + +
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Residues in contact with GLN 533 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
333B LYS* 3.5 43.8 + - + +
528B TRP 4.2 0.4 + - - -
529B TYR* 2.9 43.9 + - + +
530B LYS* 3.9 15.1 + - - +
531B LYS 4.6 3.0 + - - +
532B TYR* 1.3 79.4 - - - +
534B LYS* 1.3 61.2 + - - +
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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
------------------------------------------------------------
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