Contacts of the strand formed by residues 456 - 461 (chain C) in PDB entry 1M1D
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 TYR 456 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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418C GLN 5.9 1.3 - - - -
419C ARG* 3.1 6.1 + - + -
420C PHE* 3.1 19.5 - - + -
421C ALA 2.9 26.0 + - - -
454C ILE* 3.3 6.2 - - - +
455C GLU* 1.3 102.0 - - + +
457C LEU* 1.3 62.9 + - - +
458C LEU* 3.9 8.3 - - + -
479C ARG 5.3 0.7 + - - -
480C MET* 3.6 41.8 - - + +
499C GLU* 4.2 18.8 - - + -
500C CYS 3.3 15.9 - - - -
501C TYR* 3.8 30.4 - + + +
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Residues in contact with LEU 457 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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421C ALA* 3.5 13.0 - - + +
423C VAL* 4.9 4.3 - - + -
442C MET* 4.6 3.4 - - - -
445C PHE* 3.4 45.5 - - + -
446C LYS* 4.5 7.2 - - + -
449C MET* 3.8 15.3 - - + -
454C ILE* 4.5 2.2 - - + -
456C TYR* 1.3 79.7 - - - +
458C LEU* 1.3 63.7 + - - +
474C PHE* 3.9 25.1 - - + -
498C MET 3.8 0.2 - - - +
499C GLU* 3.1 5.4 - - - -
500C CYS* 2.8 41.9 + - + -
502C ILE* 4.1 27.6 - - + -
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Residues in contact with LEU 458 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
420C PHE* 4.4 16.4 - - + -
421C ALA 3.0 10.5 + - - +
422C GLU* 3.4 7.7 - - - +
423C VAL* 2.9 25.9 + - - +
456C TYR* 3.9 22.7 - - + -
457C LEU* 1.3 82.7 - - - +
459C THR* 1.3 62.3 + - - +
474C PHE* 4.9 0.2 - - - -
481C PRO* 4.7 24.2 - - + -
482C GLN 5.7 0.4 - - - +
489C ILE* 4.2 31.9 - - + -
497C LEU* 4.3 19.5 - - + -
498C MET 3.3 4.9 - - - +
499C GLU* 4.0 19.7 - - + +
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Residues in contact with THR 459 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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422C GLU* 5.0 3.4 - - - -
423C VAL* 2.8 27.2 + - - +
458C LEU* 1.3 77.7 - - - +
460C TYR* 1.3 57.5 + - - +
461C ALA* 4.6 3.1 - - + +
469C PHE* 3.8 34.5 - - + -
474C PHE* 4.0 11.2 - - + -
496C THR 3.4 1.2 - - - +
497C LEU* 3.6 7.0 - - - +
498C MET* 2.7 41.8 + - + +
314D LYX 2.2 33.3 + - - +
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Residues in contact with TYR 460 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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422C GLU* 4.5 6.2 + - - -
423C VAL 4.8 1.0 + - - -
459C THR* 1.3 73.3 + - - +
461C ALA* 1.3 55.5 + - - +
485C TRP 5.4 2.6 + - - -
489C ILE* 3.3 43.4 + - + -
490C LYS* 3.8 15.8 - - - -
491C ASP* 3.7 33.4 + - + +
494C GLY 3.9 18.4 - - - +
495C GLY 4.5 0.9 - - - -
496C THR 3.3 6.5 - - - +
497C LEU* 3.4 50.5 - - + +
314D LYX 2.6 42.5 + - + +
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Residues in contact with ALA 461 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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459C THR* 3.6 2.6 + - + -
460C TYR* 1.3 74.2 - - - +
462C ASP* 1.3 67.1 + - - +
465C ALA* 4.3 3.1 - - + -
466C ILE* 4.1 9.9 - - + +
469C PHE* 3.9 29.2 - - + -
496C THR* 2.6 48.7 + - - +
498C MET* 4.2 14.8 - - + -
314D LYX 4.1 6.5 - - - -
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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