Contacts of the helix formed by residues 437 - 453 (chain A) in PDB entry 4YD1
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 437 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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323A ARG* 3.5 28.0 - - - +
436A GLY* 1.3 75.1 + - - -
438A LYS* 1.3 65.8 + - - +
439A LEU 3.6 1.6 + - - -
440A PHE* 3.0 15.9 + - - +
441A GLN* 2.9 19.8 + - - +
492A ARG 3.1 22.3 + - - -
493A ASN* 4.6 1.6 - - - -
494A ALA 2.8 28.3 + - - -
607A DUP 5.1 0.2 - - - -
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Residues in contact with LYS 438 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176A LEU* 6.0 4.2 - - - +
437A SER* 1.3 74.1 - - - +
439A LEU* 1.3 64.5 + - - +
441A GLN* 3.2 2.6 + - - +
442A ARG* 3.1 44.0 + - - +
607A DUP 3.7 53.9 + - + +
5T A 3.5 25.2 - - - +
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Residues in contact with LEU 439 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142A ALA* 5.0 1.1 - - + -
177A LEU* 4.2 23.8 - - + -
180A CYS* 3.6 30.5 - - + +
181A ARG* 4.3 5.6 - - + +
184A SER* 3.5 33.7 - - - +
437A SER* 3.3 2.2 + - - -
438A LYS* 1.3 79.4 - - - +
440A PHE* 1.3 63.5 + - - +
442A ARG* 3.3 11.9 + - + +
443A GLU* 2.9 47.5 + - + +
494A ALA* 3.7 21.1 - - + +
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Residues in contact with PHE 440 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142A ALA 3.9 10.1 - - - -
143A CYS* 3.6 30.8 - - + +
147A THR* 5.7 0.7 - - - -
432A LEU* 4.9 0.4 - - + -
436A GLY 3.9 4.0 - - - -
437A SER* 3.0 30.2 + - - +
439A LEU* 1.3 76.7 - - - +
441A GLN* 1.3 77.5 + - - +
443A GLU* 3.6 4.5 - - - +
444A LEU* 2.8 42.5 + - + +
479A PHE* 4.1 18.4 - + - -
487A LEU* 3.7 23.3 - - + -
491A GLN 4.5 1.3 - - - -
492A ARG* 3.6 42.2 - - + +
494A ALA* 3.9 11.8 - - + +
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Residues in contact with GLN 441 (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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432A LEU* 3.0 40.7 + - - +
433A GLY* 3.5 29.9 - - - +
436A GLY* 3.4 20.3 + - - -
437A SER 2.9 19.1 + - - +
438A LYS 3.8 3.4 - - - +
440A PHE* 1.3 91.6 - - - +
442A ARG* 1.3 60.9 + - - +
444A LEU* 3.7 9.2 - - - +
445A ARG* 2.9 55.4 + - - +
456A LEU* 5.2 0.9 - - - +
607A DUP 4.0 14.8 - - - +
5T A 4.7 0.9 - - + -
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Residues in contact with ARG 442 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173A GLU* 4.7 15.2 + - - +
176A LEU* 3.9 22.2 - - - +
177A LEU* 3.8 22.5 - - + +
180A CYS* 5.8 1.0 - - - -
438A LYS* 3.1 39.8 + - - +
439A LEU* 3.7 20.6 - - + +
441A GLN* 1.3 76.5 - - - +
443A GLU* 1.3 59.2 + - + +
445A ARG 3.4 0.2 + - - -
446A ARG* 2.9 30.7 + - - +
5T A 3.0 100.3 + - + +
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Residues in contact with GLU 443 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140A ALA 4.0 2.9 - - - +
141A TYR* 3.5 7.0 - - - -
142A ALA* 2.9 48.4 + - + +
143A CYS* 4.0 5.6 - - - +
145A ARG* 5.0 1.0 + - - -
177A LEU* 4.7 1.7 - - - +
181A ARG* 3.0 36.9 + - - +
204A HIS* 5.1 0.3 + - - -
439A LEU* 2.9 33.1 + - + +
440A PHE 3.6 4.0 - - - +
442A ARG* 1.3 77.8 - - - +
444A LEU* 1.3 56.6 + - - +
446A ARG* 3.1 32.1 + - - +
447A PHE* 2.8 30.8 + - - +
5T A 5.2 0.9 + - - -
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Residues in contact with LEU 444 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143A CYS* 3.7 16.7 - - + -
432A LEU* 3.7 33.4 - - + -
440A PHE* 2.8 29.1 + - + +
441A GLN* 3.7 12.6 - - - +
443A GLU* 1.3 76.4 - - - +
445A ARG* 1.3 57.9 + - - +
447A PHE* 3.4 2.4 + - - +
448A SER* 2.9 28.6 + - - -
456A LEU* 3.6 24.5 - - + -
479A PHE* 4.8 7.0 - - + -
482A LEU* 3.8 11.2 - - + -
484A LEU* 3.4 33.4 - - + -
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Residues in contact with ARG 445 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
433A GLY* 4.0 12.7 - - - -
441A GLN* 2.9 31.7 + - - +
444A LEU* 1.3 73.0 - - + +
446A ARG* 1.3 65.5 + - - +
448A SER* 3.5 7.5 + - - -
449A ARG* 3.1 25.3 + - - +
454A LEU 4.9 0.2 - - - +
456A LEU* 3.6 38.7 + - + +
457A ASN* 4.0 10.1 - - - +
458A SER* 3.2 22.8 + - - +
606A EDO 3.0 26.0 + - - -
5T A 3.1 56.8 + - - +
6T A 3.3 28.7 + - - +
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Residues in contact with ARG 446 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140A ALA* 4.2 8.9 + - - +
141A TYR* 3.4 36.4 + - + -
181A ARG* 3.0 36.0 - - - +
204A HIS* 4.5 6.7 + - - -
442A ARG 2.9 17.9 + - - +
443A GLU* 3.1 35.6 + - - +
445A ARG* 1.3 76.5 - - - +
447A PHE* 1.3 57.9 + - - +
449A ARG* 3.4 2.2 + - - +
450A LYS* 2.8 52.4 + - + +
4T C 4.2 22.2 - - - -
5T A 3.8 14.0 + - - -
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Residues in contact with PHE 447 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141A TYR* 3.5 26.0 - + + -
143A CYS* 3.6 14.8 - - - -
144A GLN* 3.6 26.2 - - - -
443A GLU 2.8 17.7 + - - +
444A LEU 3.6 2.5 - - - +
446A ARG* 1.3 75.3 - - - +
448A SER* 1.3 65.8 + - - +
451A GLU* 2.8 57.3 + - + +
452A LYS* 3.3 28.8 + - + -
482A LEU* 3.4 24.9 - - + -
483A GLY 5.1 2.2 - - - -
484A LEU* 3.7 31.2 - - + -
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Residues in contact with SER 448 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
444A LEU 2.9 18.3 + - - -
445A ARG 3.7 5.4 - - - -
447A PHE* 1.3 78.8 - - - +
449A ARG* 1.3 57.9 + - - +
452A LYS* 3.0 9.2 + - - +
453A GLY 2.9 23.2 + - - -
454A LEU* 2.8 24.3 + - - +
456A LEU* 3.8 12.4 - - - +
461A LEU* 3.4 13.5 - - - +
482A LEU* 3.3 32.7 - - - +
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Residues in contact with ARG 449 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
445A ARG 3.1 15.1 + - - +
446A ARG* 4.0 2.7 - - - +
448A SER* 1.3 78.6 - - - +
450A LYS* 1.3 90.9 + - + +
453A GLY* 3.2 19.4 + - - -
454A LEU 3.2 13.7 - - - +
455A TRP* 3.3 55.2 - - + +
4T C 4.5 5.2 - - - -
5T A 5.1 1.8 - - - -
6T A 2.9 37.6 + - - +
7T T 5.4 5.3 + - - -
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Residues in contact with LYS 450 (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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141A TYR* 3.8 13.5 - - - +
446A ARG* 2.8 36.9 + - + +
449A ARG* 1.3 94.8 - - + +
451A GLU* 1.3 67.5 + - - +
453A GLY 4.9 0.2 + - - -
3T G 3.3 17.8 + - - -
4T C 2.8 39.3 + - - -
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Residues in contact with GLU 451 (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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141A TYR* 2.7 36.3 + - + +
447A PHE* 2.8 53.9 + - + +
450A LYS* 1.3 80.1 - - - +
452A LYS* 1.3 64.6 + - + +
453A GLY 3.6 0.7 - - - -
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Residues in contact with LYS 452 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
447A PHE* 3.6 30.7 - - + +
448A SER* 3.0 15.0 + - - +
451A GLU* 1.3 85.5 + - - +
453A GLY* 1.3 64.2 + - - +
454A LEU* 3.4 24.7 + - + +
481A HIS 5.7 0.9 - - - +
482A LEU* 3.2 34.1 - - + +
483A GLY* 4.7 9.7 + - - -
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Residues in contact with GLY 453 (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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448A SER 2.9 3.2 + - - -
449A ARG 3.2 17.1 + - - -
450A LYS 4.7 0.4 + - - -
451A GLU 3.6 1.2 - - - -
452A LYS* 1.3 79.2 - - - +
454A LEU* 1.3 61.6 + - - +
455A TRP* 4.6 4.7 - - - -
463A ASP* 5.0 0.3 - - - +
464A PRO* 3.2 27.7 - - - +
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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