Contacts of the helix formed by residues 514 - 522 (chain A) in PDB entry 3ZJU
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 ASP 514 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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505A CYS* 3.2 26.7 - - + +
508A TYR* 3.6 34.5 + - + -
513A LEU* 1.3 70.1 - - - +
515A SER* 1.3 62.0 + - - +
516A GLU* 3.2 17.7 + - - +
517A ALA* 3.1 17.4 + - + +
518A ALA* 2.8 27.9 + - - +
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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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513A LEU 3.6 5.9 + - - -
514A ASP* 1.3 73.8 + - - +
516A GLU* 1.3 65.7 + - - +
518A ALA* 4.4 1.8 - - - -
519A ASN* 2.9 41.9 + - - +
552A GLY 3.9 6.4 + - - -
553A MET* 3.1 36.4 + - - +
555A ASN* 6.3 0.2 - - - -
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Residues in contact with GLU 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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28A GLU* 5.0 1.2 - - - +
514A ASP* 3.2 10.1 + - - +
515A SER* 1.3 82.1 - - - +
517A ALA* 1.3 65.6 + - - +
519A ASN* 4.1 2.9 - - - +
520A TYR* 3.2 24.6 + - - +
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Residues in contact with ALA 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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28A GLU* 4.1 23.3 - - - +
504A THR* 3.5 24.2 - - - +
505A CYS* 4.2 4.0 - - + -
514A ASP* 3.1 29.9 + - + +
516A GLU* 1.3 77.5 - - - +
518A ALA* 1.3 63.6 + - - +
520A TYR* 3.3 9.7 + - - +
521A TRP* 3.4 20.3 + - - -
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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
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501A ALA 4.7 0.2 - - - +
504A THR* 3.4 21.7 + - - +
513A LEU* 4.1 27.8 - - + -
514A ASP 2.8 15.4 + - - +
515A SER* 4.0 5.4 - - - +
517A ALA* 1.3 78.1 - - - +
519A ASN* 1.3 56.6 + - - +
521A TRP* 3.9 0.5 - - - +
522A LEU* 3.0 45.9 + - + +
554A VAL* 4.2 6.5 - - + -
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Residues in contact with ASN 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 27.0 + - - +
516A GLU* 4.5 2.9 - - - +
518A ALA* 1.3 74.2 - - - +
520A TYR* 1.3 64.4 + - - +
521A TRP 3.4 0.2 - - - -
522A LEU* 3.5 17.0 + - - +
553A MET 4.2 1.4 - - - +
554A VAL* 3.5 18.5 - - - +
555A ASN* 2.9 51.8 + - + +
556A SER* 4.7 4.0 + - - +
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Residues in contact with TYR 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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28A GLU* 3.8 18.4 - - + -
29A ASP 2.8 42.4 + - - -
30A GLU* 3.9 28.5 - - - +
32A LYS 3.9 6.5 + - - -
34A LYS* 3.4 47.4 - - + +
72A ASN* 2.9 18.7 + - - -
516A GLU 3.2 19.4 + - - +
517A ALA 3.3 4.7 + - - +
519A ASN* 1.3 80.0 - - - +
521A TRP* 1.3 96.4 + + - +
522A LEU 4.3 0.5 - - - +
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Residues in contact with TRP 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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26A VAL* 3.8 22.2 - - + -
27A THR 3.6 19.5 - - - -
28A GLU* 2.7 28.0 + - + +
34A LYS* 2.7 35.8 + - + +
35A TYR 3.8 5.6 - - - -
36A TYR* 3.6 23.2 - - + +
72A ASN* 3.4 38.8 - - - -
74A LEU* 3.4 38.4 - - + -
123A ARG* 4.2 4.7 - - - +
504A THR* 3.7 32.5 - - + -
517A ALA 3.4 20.8 + - - -
520A TYR* 1.3 93.4 - + - +
522A LEU* 1.3 57.7 + - - +
523A PRO 3.2 4.0 - - - +
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Residues in contact with LEU 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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34A LYS* 4.1 5.2 + - - -
36A TYR* 4.0 21.1 - - + -
500A TYR* 3.9 28.9 - - + +
501A ALA* 4.4 14.6 - - + -
504A THR* 4.6 4.5 - - + -
518A ALA* 3.0 28.6 + - + +
519A ASN* 3.5 18.6 + - - +
520A TYR 4.3 0.9 - - - +
521A TRP* 1.3 79.7 - - - +
523A PRO* 1.3 69.1 - - + +
524A VAL 4.0 9.2 - - - +
545A HIS* 4.0 14.4 - - + -
554A VAL* 4.0 26.0 - - + -
556A SER* 4.8 7.9 - - - +
559A PRO 4.5 0.9 - - - +
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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