Contacts of the helix formed by residues 516 - 531 (chain A) in PDB entry 1H7B
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 ASN 516 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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512A ASP 5.0 1.8 - - - +
513A MET* 2.9 50.4 + - + +
515A ASN* 1.3 79.7 - - - +
517A LEU* 1.3 61.7 + - - +
518A LYS* 3.3 3.5 + - - +
519A GLY* 3.0 22.2 + - - -
520A LEU 3.3 0.5 + - - -
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Residues in contact with LEU 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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255A GLN* 4.3 14.4 - - - +
258A LEU* 4.2 17.4 - - + +
259A GLU* 3.7 42.2 - - + +
262A SER* 4.6 5.2 - - - +
513A MET 3.5 7.9 - - - +
514A LYS* 2.8 31.6 - - - +
515A ASN* 3.8 2.4 - - - -
516A ASN* 1.3 74.5 - - - +
518A LYS* 1.3 59.6 + - - +
520A LEU* 3.2 6.6 + - + +
521A GLU* 2.8 30.9 + - - +
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Residues in contact with LYS 518 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
246A LYS* 4.0 20.4 - - - +
251A TYR* 3.4 23.6 + - - -
255A GLN* 4.9 2.4 - - - +
516A ASN* 3.3 3.3 - - - +
517A LEU* 1.3 77.9 - - - +
519A GLY* 1.3 58.4 + - - +
521A GLU* 3.7 16.4 + - - +
522A ALA* 3.2 23.7 + - - +
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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
----------------------------------------------------------
513A MET* 3.6 9.4 - - - -
516A ASN* 3.0 25.5 + - - -
517A LEU 3.0 0.8 - - - -
518A LYS* 1.3 75.4 - - - +
520A LEU* 1.3 64.0 + - - +
522A ALA* 3.1 21.5 - - - +
523A VAL* 3.3 12.5 + - - +
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Residues in contact with LEU 520 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
258A LEU* 3.6 36.3 - - + +
261A ALA* 4.3 11.9 - - + -
262A SER* 4.3 8.1 - - - +
510A LEU* 4.6 2.5 - - + -
513A MET* 3.3 18.0 - - + +
516A ASN 3.3 3.3 + - - +
517A LEU* 3.2 10.0 + - - +
519A GLY* 1.3 73.0 - - - +
521A GLU* 1.3 66.9 + - - +
522A ALA 3.1 0.2 + - - -
523A VAL* 3.2 6.6 + - + +
524A TRP* 2.9 49.6 + - + +
536A VAL* 4.0 15.3 - - + -
538A MET* 3.3 26.7 - - + -
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Residues in contact with GLU 521 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
244A LEU 4.1 1.2 - - - +
246A LYS* 4.1 6.2 - - - -
251A TYR* 2.9 23.3 + - - -
254A LYS* 2.9 33.7 + - - +
255A GLN* 3.1 21.3 + - - +
258A LEU* 3.6 18.4 - - + +
517A LEU 2.8 17.8 + - - +
518A LYS* 3.8 26.1 + - + +
519A GLY 3.2 0.2 - - - -
520A LEU* 1.3 76.8 - - - +
522A ALA* 1.3 55.2 + - - +
524A TRP* 3.4 2.7 + - - +
525A ASP* 2.8 49.9 + - - +
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Residues in contact with ALA 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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487A PHE* 4.1 16.9 - - + -
518A LYS 3.2 14.2 + - - +
519A GLY* 3.1 14.6 - - - +
521A GLU* 1.3 75.3 - - - +
523A VAL* 1.3 65.0 + - - +
525A ASP* 3.2 7.9 + - - +
526A TYR* 2.9 23.6 + - - +
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Residues in contact with VAL 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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486A PRO* 4.5 12.6 - - + -
487A PHE* 4.4 16.1 - - + -
490A ILE* 3.8 10.0 - - + +
508A VAL* 4.4 13.5 - - + -
510A LEU* 4.2 26.0 - - + -
513A MET* 5.8 0.2 - - + -
519A GLY 3.5 13.7 - - - +
520A LEU* 3.2 8.7 + - + +
522A ALA* 1.3 74.2 - - - +
524A TRP* 1.3 64.1 + - - +
526A TYR* 3.1 3.4 + - - +
527A ALA* 2.9 23.0 + - - +
534A PHE* 3.5 28.7 - - + -
536A VAL* 4.6 4.5 - - + -
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Residues in contact with TRP 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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236A MET* 5.4 1.1 - - - -
238A VAL* 5.2 7.6 - - + -
254A LYS* 4.1 26.0 - - + -
257A ALA* 3.8 15.9 - - + -
258A LEU* 3.6 41.3 - - + -
261A ALA* 3.8 23.9 - - + +
267A PRO* 4.0 10.6 + - + -
269A ILE* 3.7 48.2 - - + +
520A LEU* 2.9 38.1 + - + +
521A GLU* 3.4 9.6 - - - +
523A VAL* 1.3 76.9 - - - +
525A ASP* 1.3 59.8 + - - +
527A ALA* 3.4 1.6 + - - +
528A ALA* 2.8 32.9 + - - +
534A PHE* 4.1 6.2 - + - -
535A GLY* 6.0 0.6 - - - -
536A VAL* 3.9 19.2 - - + +
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Residues in contact with ASP 525 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
244A LEU* 3.9 20.0 - - + +
245A TYR* 6.4 1.8 - - - -
246A LYS* 4.7 7.9 + - - -
254A LYS* 2.7 25.6 + - - -
521A GLU* 2.8 42.2 + - - +
522A ALA* 3.7 6.1 - - - +
524A TRP* 1.3 72.6 - - - +
526A TYR* 1.3 63.0 + - - +
528A ALA* 3.7 6.2 - - - +
529A GLN* 3.2 22.3 + - - +
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Residues in contact with TYR 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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487A PHE* 3.2 59.4 + + + +
490A ILE* 3.5 33.0 - - + -
491A SER* 3.7 19.9 + - - -
522A ALA 2.9 13.2 + - - +
523A VAL 3.1 7.2 + - - +
525A ASP* 1.3 75.4 - - - +
527A ALA* 1.3 64.4 + - - +
529A GLN* 3.2 3.3 + - - +
530A HIS* 3.1 61.6 + + - +
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Residues in contact with ALA 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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269A ILE* 5.1 0.7 - - + -
490A ILE* 3.7 17.1 - - + +
523A VAL 2.9 13.9 + - - +
524A TRP 3.8 2.0 - - - +
526A TYR* 1.3 75.1 - - - +
528A ALA* 1.3 59.3 + - - +
530A HIS 3.2 0.2 + - - -
531A LEU* 2.7 48.1 + - + +
534A PHE* 3.5 43.7 - - + -
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Residues in contact with ALA 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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238A VAL* 4.1 25.6 - - + -
244A LEU* 4.7 12.8 - - + -
269A ILE* 4.7 6.0 - - + +
271A SER* 2.7 34.4 + - - +
273A LYS* 4.8 1.4 - - - +
274A ASN* 3.0 4.2 + - - -
524A TRP 2.8 21.9 + - - +
525A ASP* 3.7 10.1 - - - +
527A ALA* 1.3 72.8 - - - +
529A GLN* 1.3 61.4 + - - +
531A LEU 4.5 0.2 - - - -
532A ASP 5.9 0.2 - - - -
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Residues in contact with GLN 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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244A LEU* 5.9 4.2 - - - +
245A TYR* 5.3 6.1 + - - -
273A LYS* 2.8 37.3 + - - +
274A ASN* 2.8 22.8 + - - +
525A ASP 3.2 15.0 + - - +
526A TYR* 3.7 4.7 - - + +
528A ALA* 1.3 80.9 - - - +
530A HIS* 1.3 74.8 + - + +
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Residues in contact with HIS 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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274A ASN* 3.7 2.0 - - - -
490A ILE* 4.4 10.3 - - + +
491A SER* 5.1 7.4 - - - -
494A ALA* 3.3 25.5 - - + +
498A PHE* 3.5 16.1 - - - -
526A TYR* 3.1 58.7 + + - +
527A ALA 4.2 0.4 - - - +
529A GLN* 1.3 94.5 - - + +
531A LEU* 1.3 59.5 + - - +
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Residues in contact with LEU 531 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
271A SER* 3.2 14.2 - - - -
274A ASN* 3.0 21.2 + - - +
490A ILE* 3.8 32.5 - - + +
494A ALA* 3.9 8.7 - - + -
497A HIS* 3.4 33.2 - - + +
498A PHE* 4.4 4.9 - - - -
506A SER* 3.8 17.0 - - - +
527A ALA* 2.7 38.0 + - + +
530A HIS* 1.3 75.3 - - - +
532A ASP* 1.3 63.5 + - - +
533A TYR 4.1 0.4 - - - +
534A PHE* 3.6 32.3 - - + -
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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
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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