Contacts of the helix formed by residues 511 - 521 (chain A) in PDB entry 4MXP
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 511 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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509A ASN* 3.7 14.8 + - - +
510A VAL* 1.3 76.3 - - - +
512A ASP* 1.3 65.6 + - - +
513A GLU* 3.0 14.7 + - - +
514A THR* 2.9 44.8 + - - +
515A LEU* 3.0 29.1 + - - +
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Residues in contact with ASP 512 (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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464A LYS* 4.3 21.9 + - - +
511A ASN* 1.3 76.1 - - - +
513A GLU* 1.3 57.9 - - - +
515A LEU* 3.8 4.4 - - - +
516A GLU* 2.8 32.4 + - - +
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Residues in contact with GLU 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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511A ASN* 3.0 10.2 + - - +
512A ASP* 1.3 79.9 - - - +
514A THR* 1.3 66.7 + - + +
516A GLU* 3.3 7.1 + - - +
517A SER* 3.1 29.8 + - - +
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Residues in contact with THR 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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504A LEU* 3.7 18.0 - - + +
509A ASN* 2.7 45.1 + - - +
510A VAL* 3.6 2.6 - - - -
511A ASN* 2.9 36.8 + - - +
513A GLU* 1.3 81.8 - - + +
515A LEU* 1.3 61.5 + - - +
517A SER* 3.5 13.4 + - - -
518A VAL* 3.5 17.5 + - - +
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Residues in contact with LEU 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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464A LYS* 4.2 29.6 - - + +
465A SER* 4.6 2.7 - - - +
468A LEU* 3.9 29.4 - - + -
501A ILE* 4.1 31.9 - - + -
504A LEU* 4.3 10.1 - - + -
510A VAL* 3.9 28.3 - - + -
511A ASN 3.0 23.8 + - - +
512A ASP* 3.9 2.7 - - - +
514A THR* 1.3 76.0 - - - +
516A GLU* 1.3 66.1 + - - +
518A VAL* 3.1 4.9 + - - +
519A LEU* 2.9 31.2 + - + +
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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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415A ASP* 5.1 1.4 - - - +
418A ARG* 3.5 24.7 + - - -
419A ALA* 3.5 27.9 - - - +
512A ASP 2.8 20.2 + - - +
513A GLU* 3.3 8.3 + - - +
515A LEU* 1.3 78.5 - - - +
517A SER* 1.3 57.3 + - - +
519A LEU* 4.1 7.3 - - - +
520A SER* 3.0 37.4 + - - +
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Residues in contact with SER 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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513A GLU* 3.1 18.7 + - - +
514A THR* 3.8 10.0 - - - -
515A LEU 3.2 0.4 - - - -
516A GLU* 1.3 76.5 - - - +
518A VAL* 1.3 63.4 + - - +
520A SER* 3.5 6.7 + - - -
521A SER* 3.4 22.2 + - - -
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Residues in contact with VAL 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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472A MET* 4.6 0.7 - - + -
497A LYS* 3.2 59.7 + - + +
500A ALA* 3.9 20.6 - - + -
501A ILE* 4.1 16.6 - - + -
504A LEU* 4.1 15.9 - - + -
514A THR 3.6 14.4 - - - +
515A LEU* 3.1 6.8 + - - +
517A SER* 1.3 75.2 - - - +
519A LEU* 1.3 65.9 + - + +
521A SER* 3.2 11.3 + - - -
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Residues in contact with LEU 519 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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412A ALA 5.3 0.2 - - - +
415A ASP* 4.9 5.2 - - + -
416A TYR* 3.8 39.9 - - + +
419A ALA* 3.8 18.2 - - + -
420A ALA* 3.7 17.8 - - - +
464A LYS* 5.6 3.1 - - - +
468A LEU* 4.0 32.5 - - + -
472A MET* 3.6 29.2 - - + -
497A LYS* 3.0 18.1 + - - +
501A ILE* 4.6 4.5 - - + -
515A LEU* 2.9 25.8 + - + +
516A GLU* 4.1 4.9 - - - +
518A VAL* 1.3 75.6 - - - +
520A SER* 1.3 57.2 + - - +
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Residues in contact with SER 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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419A ALA* 3.2 26.7 - - - -
420A ALA* 4.5 0.2 - - - +
422A THR* 3.6 21.8 + - - +
516A GLU* 3.0 28.1 + - - +
517A SER* 3.5 8.5 + - - -
519A LEU* 1.3 76.0 - - - +
521A SER* 1.3 65.7 + - - +
522A LYS* 3.6 7.4 + - - +
524A GLU* 4.7 2.4 - - - +
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Residues in contact with SER 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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493A LEU* 5.3 1.1 - - - +
496A HIS* 5.6 4.7 - - - -
497A LYS* 2.7 35.5 + - - -
517A SER 3.4 16.2 + - - -
518A VAL* 3.2 12.5 + - - -
520A SER* 1.3 80.6 + - - +
522A LYS* 1.3 62.3 + - - +
523A GLY* 3.1 19.8 + - - -
524A GLU* 3.9 6.2 + - - -
528A GLU* 5.7 0.7 + - - -
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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