Contacts of the helix formed by residues 448 - 453 (chain D) in PDB entry 5M8N
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 THR 448 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69D THR* 5.4 4.9 - - + +
436D ARG 4.1 1.8 - - - -
437D GLN* 3.4 36.9 + - - +
438D TYR 3.2 7.6 - - - -
439D ASN* 3.3 18.4 - - - +
440D MET* 3.7 9.0 - - - +
447D VAL* 1.3 75.2 - - - +
449D ASN* 1.3 65.0 + - - +
450D THR* 3.1 15.1 + - - -
451D GLU* 2.5 50.4 + - - +
452D MET 4.0 0.7 + - - -
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Residues in contact with ASN 449 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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219D ALA* 3.1 14.8 - - - +
222D THR* 2.7 38.4 + - - +
425D PHE* 3.6 24.0 - - + -
433D GLY 3.3 19.2 + - - -
434D HIS 4.4 0.4 - - - -
435D ASN 3.1 21.6 + - - -
436D ARG* 3.4 9.8 + - + +
438D TYR* 3.2 18.8 + - - +
440D MET* 3.4 22.2 - - - +
448D THR* 1.3 72.6 - - - +
450D THR* 1.3 64.1 + - - +
452D MET* 3.1 10.7 + - - +
453D PHE* 3.5 1.9 + - - +
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Residues in contact with THR 450 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
345A PRO* 6.5 0.9 - - + -
422D ILE* 3.9 24.0 - - + -
436D ARG* 3.0 18.7 + - - +
437D GLN* 2.3 32.4 + - - +
448D THR* 3.0 9.0 - - - -
449D ASN* 1.3 78.2 - - - +
451D GLU* 1.3 64.6 + - + +
453D PHE* 3.0 20.6 + - - +
454D VAL* 4.7 2.6 - - - +
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Residues in contact with GLU 451 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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446D PRO 4.5 2.3 - - - +
447D VAL* 3.4 22.6 - - + +
448D THR* 2.5 49.5 + - - +
450D THR* 1.3 76.3 - - + +
452D MET* 1.3 67.8 + - + +
454D VAL* 3.3 21.7 - - - +
460D LEU* 4.5 2.8 - - - +
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Residues in contact with MET 452 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115D PRO* 5.9 1.1 - - + -
222D THR* 3.6 40.4 - - + +
225D ARG* 3.3 47.4 + - - -
226D TYR* 3.8 32.1 - - + -
229D LEU* 4.2 9.6 - - + -
411D PHE* 4.3 2.3 - - - -
440D MET* 3.9 19.7 - - + -
447D VAL* 4.4 9.6 - - + -
448D THR 4.6 0.2 - - - +
449D ASN 3.1 2.0 + - - +
450D THR 3.0 0.4 - - - -
451D GLU* 1.3 90.1 - - + +
453D PHE* 1.3 49.9 + - - +
454D VAL* 2.7 21.5 + - - +
460D LEU* 4.2 17.0 - - + -
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Residues in contact with PHE 453 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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222D THR* 4.0 4.5 - - + +
342D PHE* 3.5 39.5 - + - -
411D PHE* 4.0 13.5 - + - -
414D TRP* 3.6 22.0 - + - -
415D LEU* 3.5 20.9 - - + -
420D ALA* 3.5 32.8 - - - +
421D ASP 3.6 11.7 - - - -
422D ILE* 3.7 28.8 - - + +
425D PHE* 3.8 18.2 - + - -
449D ASN 3.5 6.3 + - - +
450D THR* 3.0 13.1 + - - +
452D MET* 1.3 74.4 - - - +
454D VAL* 1.3 66.2 + - - +
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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