Contacts of the helix formed by residues 509 - 523 (chain A) in PDB entry 4K4I
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 509 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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420A ARG* 3.8 27.1 - - - +
507A THR 3.7 0.6 + - - -
508A GLY* 1.3 75.1 + - - -
510A ALA* 1.3 55.3 + - - +
511A HIS* 3.4 5.5 + - - +
512A PHE* 3.1 13.3 + - - +
513A ASN* 2.8 32.8 + - - +
573A ARG 3.1 15.9 + - - -
574A ASP* 2.7 27.8 + - - -
601A 1RY 4.7 2.9 - - - -
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Residues in contact with ALA 510 (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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508A GLY* 4.1 0.6 - - - -
509A SER* 1.3 74.8 - - - +
511A HIS* 1.3 61.3 + - + +
513A ASN* 3.1 3.6 + - - +
514A ARG* 2.9 36.2 + - + +
601A 1RY 3.5 56.8 + - + +
5B G 5.4 0.7 - - - +
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Residues in contact with HIS 511 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277A LEU* 4.2 21.3 - - + +
280A ALA* 4.2 17.5 - - + +
281A LYS* 5.3 4.4 - - + -
509A SER* 3.4 7.8 + - - +
510A ALA* 1.3 76.3 - - + +
512A PHE* 1.3 65.3 + - - +
514A ARG* 3.5 19.6 + - - +
515A SER* 3.1 27.4 + - - -
574A ASP 4.1 3.6 - - - +
575A TRP* 3.3 54.6 - + + -
576A LEU 5.3 0.4 - - - -
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Residues in contact with PHE 512 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
504A LEU* 4.4 5.4 - - + -
508A GLY 3.8 12.8 - - - -
509A SER* 3.1 13.7 + - - +
511A HIS* 1.3 77.1 - - - +
513A ASN* 1.3 64.8 + - - +
515A SER* 3.4 2.3 + - - -
516A MET* 3.0 54.5 + - + +
560A PHE* 3.8 28.7 - + - -
568A ARG* 4.2 10.5 - - + -
573A ARG* 3.4 60.8 - - + +
574A ASP 4.0 2.1 + - - +
575A TRP 3.9 0.7 - - - -
576A LEU* 3.8 44.8 - - + +
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Residues in contact with ASN 513 (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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504A LEU* 3.4 18.4 - - - +
505A TYR* 2.9 35.9 + - - +
508A GLY* 3.5 7.9 - - - -
509A SER 2.8 17.6 + - - +
510A ALA 3.1 5.8 + - - +
512A PHE* 1.3 80.9 - - - +
514A ARG* 1.3 57.8 + - - +
516A MET* 3.3 7.4 + - - +
517A ARG* 2.9 40.1 + - - +
527A LEU* 6.2 0.2 - - - -
601A 1RY 2.9 31.8 + - - +
5B G 4.0 7.6 - - - +
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Residues in contact with ARG 514 (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 TRP* 4.4 6.3 - - - -
277A LEU* 3.9 35.2 - - - +
281A LYS* 6.2 2.0 - - - +
510A ALA* 2.9 22.6 + - - +
511A HIS* 3.7 21.0 + - - +
513A ASN* 1.3 77.4 - - - +
515A SER* 1.3 57.9 + - - +
517A ARG* 3.3 2.4 + - - +
518A ALA* 2.8 31.1 + - - +
5B G 3.0 92.5 + - + +
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Residues in contact with SER 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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281A LYS* 5.6 6.9 + - - -
511A HIS* 3.1 16.2 + - - +
512A PHE 3.8 0.9 - - - -
514A ARG* 1.3 75.4 - - - +
516A MET* 1.3 61.5 + - - +
518A ALA* 3.5 6.4 + - - +
519A LEU* 2.9 29.3 + - - +
576A LEU* 3.7 23.8 - - - +
577A GLU* 3.0 30.7 + - - -
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Residues in contact with MET 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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504A LEU* 3.4 37.0 - - + -
512A PHE* 3.0 44.9 + - + +
513A ASN* 3.5 8.3 - - - +
515A SER* 1.3 75.2 - - - +
517A ARG* 1.3 58.3 + - - +
519A LEU* 3.2 7.2 + - - +
520A ALA* 3.0 27.4 + - - +
527A LEU* 3.8 11.6 - - + +
559A VAL* 4.8 2.2 - - + -
560A PHE* 4.0 19.3 - - + -
563A LEU* 4.2 21.6 - - + +
565A LEU* 3.9 26.2 - - - -
576A LEU* 4.5 6.9 - - + +
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Residues in contact with ARG 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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505A TYR* 3.3 27.3 - - - +
513A ASN* 2.9 22.0 + - - +
514A ARG 3.6 3.8 - - - +
516A MET* 1.3 74.6 - - - +
518A ALA* 1.3 66.0 + - - +
520A ALA* 3.2 4.3 + - - +
521A LYS* 3.1 21.7 + - - +
527A LEU* 3.2 44.4 + - + +
528A SER* 3.6 2.6 - - - +
529A GLU* 3.2 39.6 + - - +
5B G 3.4 44.9 - - - +
6B G 3.0 44.2 + - - -
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Residues in contact with ALA 518 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
514A ARG 2.8 20.8 + - - +
515A SER* 3.9 6.5 - - - +
517A ARG* 1.3 72.8 - - - +
519A LEU* 1.3 62.5 + - - +
521A LYS* 3.6 9.1 + - - +
522A THR* 3.2 25.4 + - - +
4B C 5.6 2.7 - - - +
5B G 3.8 17.5 - - - -
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Residues in contact with LEU 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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515A SER 2.9 17.9 + - - +
516A MET* 3.5 5.6 - - - +
517A ARG 3.1 0.4 - - - -
518A ALA* 1.3 74.0 - - - +
520A ALA* 1.3 66.7 + - - +
522A THR* 2.4 32.1 + - + +
523A LYS* 3.2 22.1 + - - +
563A LEU* 3.6 31.2 - - + +
565A LEU* 3.8 31.6 - - + -
576A LEU* 5.0 8.7 - - + -
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Residues in contact with ALA 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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516A MET 3.0 12.4 + - - +
517A ARG 3.2 8.3 + - - +
519A LEU* 1.3 75.9 - - - +
521A LYS* 1.3 62.7 + - - +
523A LYS* 3.1 8.2 + - - -
525A MET* 2.8 34.5 + - + +
527A LEU* 4.0 29.6 - - + +
532A LEU* 4.3 0.9 - - + -
563A LEU* 3.8 26.2 - - + +
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Residues in contact with LYS 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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517A ARG 3.1 14.7 + - - +
518A ALA* 3.9 8.5 - - - +
519A LEU 3.2 0.2 - - - -
520A ALA* 1.3 72.5 - - - +
522A THR* 1.3 65.1 + - - +
523A LYS 3.0 2.3 + - - -
524A GLY* 3.1 11.3 + - - -
525A MET 3.3 13.2 + - - +
4B C 2.6 34.0 + - - +
5B G 4.2 7.6 + - - -
6B G 3.0 39.9 + - - +
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Residues in contact with THR 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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518A ALA* 3.2 14.9 + - + +
519A LEU* 2.4 34.7 + - + +
521A LYS* 1.3 76.2 - - - +
523A LYS* 1.3 62.6 + - - +
524A GLY 3.4 2.1 + - - -
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Residues in contact with LYS 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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519A LEU* 3.6 29.4 - - + +
520A ALA 3.1 3.6 + - - +
521A LYS 3.0 1.4 - - - -
522A THR* 1.3 81.9 + - - +
524A GLY* 1.3 60.7 - - - +
525A MET* 3.2 33.3 + - + +
534A THR* 5.4 1.7 - - - +
562A LEU 4.9 1.0 + - - +
563A LEU* 3.2 36.5 + - + +
564A GLY* 4.4 5.5 - - - +
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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