Contacts of the helix formed by residues 434 - 445 (chain A) in PDB entry 4Z4Q
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 GLY 434 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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432A VAL 3.2 1.9 + - - +
433A GLU* 1.3 75.8 - - - +
435A ASP* 1.3 60.9 + - - -
436A SER* 3.1 4.3 - - - -
437A ALA 4.0 1.8 - - - -
438A GLY* 2.8 27.1 + - - -
454A PRO* 3.8 6.4 - - - +
455A LEU 3.0 20.0 + - - -
456A ARG* 5.0 2.2 - - - -
457A GLY 5.2 1.7 - - - +
1118B TYR* 5.5 8.1 - - - -
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Residues in contact with ASP 435 (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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434A GLY* 1.3 70.6 - - - -
436A SER* 1.3 57.9 + - - +
438A GLY* 3.1 1.7 + - - -
439A GLY* 2.8 26.5 + - - -
454A PRO* 3.4 26.5 - - - +
455A LEU 4.6 1.4 + - - -
456A ARG* 3.2 45.3 + - + +
1118B TYR* 5.7 0.6 + - - -
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Residues in contact with SER 436 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
434A GLY* 3.1 1.2 - - - -
435A ASP* 1.3 79.3 - - - +
437A ALA* 1.3 62.3 + - - +
439A GLY 3.1 8.8 + - - -
440A SER 3.2 2.8 + - - -
584A GLY* 6.1 2.7 - - - -
1104B ASN* 3.2 25.0 + - - +
1114B ALA* 3.7 25.3 - - - +
1115B ALA 4.1 1.0 + - - -
1118B TYR* 3.2 44.7 + - - -
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Residues in contact with ALA 437 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
432A VAL* 3.5 17.9 - - + +
433A GLU 3.6 13.5 - - - +
434A GLY* 3.5 3.2 + - - -
436A SER* 1.3 74.4 - - - +
438A GLY* 1.3 56.4 + - - +
439A GLY 3.0 1.8 - - - -
440A SER* 3.0 9.4 + - - +
441A ALA* 2.7 36.9 + - - +
504A MET* 5.7 0.2 - - + -
506A ASP* 5.7 0.2 - - - +
583A LEU* 3.9 32.5 - - + -
584A GLY* 5.1 4.4 - - - +
591A LEU* 4.7 3.3 - - + +
1118B TYR* 5.9 0.4 - - - -
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Residues in contact with GLY 438 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
432A VAL* 3.2 17.1 - - - +
434A GLY 2.8 16.2 + - - -
435A ASP 3.1 5.8 + - - -
437A ALA* 1.3 75.4 - - - +
439A GLY* 1.3 55.9 + - - +
441A ALA* 3.4 3.2 - - - +
442A LYS* 2.9 30.1 + - - +
452A ILE* 3.7 6.7 - - - +
454A PRO* 4.2 16.4 - - - -
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Residues in contact with GLY 439 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
435A ASP 2.8 13.4 + - - -
436A SER 3.1 6.0 + - - -
437A ALA 3.0 1.4 - - - -
438A GLY* 1.3 72.2 - - - +
440A SER* 1.3 64.2 + - - -
442A LYS* 3.1 7.5 + - - +
443A GLN* 3.0 31.4 + - - +
1104B ASN* 3.6 13.5 - - - -
1111B ASP* 5.7 4.3 - - - -
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Residues in contact with SER 440 (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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436A SER 3.2 7.3 + - - -
437A ALA* 3.0 10.6 + - - -
439A GLY* 1.3 72.1 - - - +
441A ALA* 1.3 53.0 + - - +
443A GLN* 3.2 14.5 + - - +
444A GLY* 2.8 33.8 + - - -
583A LEU 5.1 3.5 + - - -
584A GLY* 5.7 1.6 + - - -
586A MET 3.8 18.2 + - - -
588A ALA* 3.7 10.5 + - - +
591A LEU* 3.8 18.5 - - - +
1103B GLY 4.5 0.5 - - - -
1104B ASN* 3.3 26.6 + - - +
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Residues in contact with ALA 441 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
432A VAL* 3.8 20.0 - - + -
437A ALA 2.7 20.8 + - - +
438A GLY 3.4 4.9 - - - +
440A SER* 1.3 71.6 - - - +
442A LYS* 1.3 64.3 + - - +
444A GLY* 3.0 10.9 + - - -
445A ARG* 3.1 17.5 + - - +
452A ILE* 3.7 22.0 - - + -
504A MET* 4.2 9.6 - - + -
591A LEU* 3.9 3.7 - - - +
596A MET* 4.2 12.3 - - - +
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Residues in contact with LYS 442 (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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417A THR* 4.0 31.9 - - + +
438A GLY 2.9 20.5 + - - +
439A GLY* 3.1 7.4 + - - +
441A ALA* 1.3 72.8 - - - +
443A GLN* 1.3 62.9 + - + +
445A ARG* 3.0 36.9 + - - +
452A ILE* 4.0 6.9 - - + +
1111B ASP* 5.2 9.2 - - - +
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Residues in contact with GLN 443 (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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439A GLY 3.0 18.9 + - - +
440A SER* 3.4 8.2 + - - +
442A LYS* 1.3 80.1 - - + +
444A GLY* 1.3 58.8 + - - +
445A ARG 4.7 0.9 - - - +
588A ALA* 3.9 16.9 - - + +
1104B ASN* 3.4 28.9 + - - +
1106B GLY 3.6 17.2 + - - +
1107B SER* 4.3 10.0 - - - -
1111B ASP* 3.2 33.5 + - - +
1292B ASP* 5.4 0.9 - - - -
1293B ARG* 4.3 19.4 + - - +
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Residues in contact with GLY 444 (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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440A SER 2.8 19.1 + - - -
441A ALA 3.0 1.9 + - - -
443A GLN* 1.3 72.9 - - - +
445A ARG* 1.3 61.3 + - - +
588A ALA* 3.8 23.1 - - - -
591A LEU* 5.6 0.9 - - - -
592A TRP* 3.3 21.9 - - - +
596A MET* 4.6 5.4 - - - -
1293B ARG* 3.0 21.2 + - - -
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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
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417A THR* 3.4 24.3 - - - +
418A PRO 3.2 26.1 + - - -
441A ALA 3.1 8.4 + - - +
442A LYS* 3.0 38.5 + - - +
443A GLN 3.5 2.2 - - - +
444A GLY* 1.3 76.9 - - - +
446A ASP* 1.3 61.4 + - - +
447A ARG* 3.6 48.9 + - + +
450A GLN* 3.0 39.5 + - + +
452A ILE* 3.8 11.8 - - + +
592A TRP* 4.1 3.8 - - - -
596A MET* 3.9 12.6 - - + -
1292B ASP* 4.9 4.2 - - - +
1293B ARG* 2.7 26.1 + - - -
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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