Contacts of the strand formed by residues 455 - 465 (chain A) in PDB entry 1MD9
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 VAL 455 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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449A LEU* 3.2 33.7 - - + +
450A LEU* 4.0 13.1 - - + +
452A HIS* 2.7 18.5 + - + +
453A PRO 3.4 0.4 - - - -
454A ALA* 1.3 75.0 - - - +
456A HIS* 1.3 60.9 + - - +
457A ASP 3.6 25.8 - - - +
458A ALA* 4.5 4.0 - - + -
476A ILE* 3.4 26.0 - - + -
477A ILE 4.1 2.0 - - - -
479A ARG* 3.2 20.3 + - - -
483A PRO* 5.1 0.9 - - + -
488A LEU* 3.9 26.0 - - + -
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Residues in contact with HIS 456 (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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281A PRO 4.9 2.5 - - - -
284A MSE 3.4 36.9 - - + +
285A VAL* 3.9 20.1 + - + +
288A ASP* 2.8 30.5 + - - -
450A LEU* 4.1 6.0 - - - +
455A VAL* 1.3 75.7 - - - +
457A ASP* 1.3 63.6 + - + +
477A ILE* 2.7 44.8 + - + +
478A PRO 4.0 2.2 - - - +
479A ARG* 3.5 34.1 + - + +
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Residues in contact with ASP 457 (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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280A PRO 5.9 0.2 - - - -
281A PRO* 4.0 21.7 - - - +
284A MSE 4.2 16.0 - - + +
450A LEU* 3.6 15.2 - - - +
455A VAL* 3.6 9.0 - - - +
456A HIS* 1.3 94.8 - - + +
458A ALA* 1.3 79.3 + - - +
476A ILE* 3.8 0.7 - - - -
477A ILE* 3.2 26.4 + - + +
512A PHE* 3.5 25.9 - - + -
520A VAL* 4.6 2.1 - - - +
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Residues in contact with ALA 458 (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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446A GLU* 3.1 28.9 - - + +
449A LEU* 4.6 10.8 - - + -
450A LEU* 4.0 8.2 - - + +
455A VAL* 4.5 6.5 - - + -
457A ASP* 1.3 91.6 + - - +
459A ALA* 1.3 61.2 + - - +
474A VAL* 4.3 5.2 - - + -
475A PHE 3.3 12.8 - - - +
476A ILE* 3.6 18.2 - - + -
512A PHE* 3.6 5.3 - - - -
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Residues in contact with ALA 459 (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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446A GLU* 3.5 5.6 - - - -
458A ALA* 1.3 75.2 - - - +
460A MSE 1.3 64.3 + - - +
461A VAL* 3.4 4.2 + - - +
474A VAL* 4.4 0.4 - - - -
475A PHE* 3.1 33.9 + - - -
512A PHE* 3.7 14.1 - - + -
520A VAL* 4.2 9.9 - - + -
522A LYS* 4.0 12.6 - - - -
525A LEU* 3.5 26.5 - - + -
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Residues in contact with MSE 460 (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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431A ASP 4.9 2.1 - - - +
433A ILE* 3.2 28.3 - - + +
440A VAL* 3.3 26.5 - - + -
442A ALA* 3.5 21.9 - - + +
445A VAL* 3.7 34.3 - - + -
446A GLU* 2.9 19.7 + - + +
459A ALA* 1.3 70.7 - - - +
461A VAL* 1.3 61.9 + - - +
472A SER* 3.3 22.2 - - - +
473A CYS 3.9 7.6 - - - +
474A VAL* 3.9 19.4 - - + +
500A TYR 5.7 0.2 - - - +
501A LYS 4.0 9.4 - - - +
503A PRO* 4.5 8.3 - - + -
522A LYS* 3.3 20.3 + - - +
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Residues in contact with VAL 461 (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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431A ASP 5.9 1.1 - - - -
433A ILE* 3.7 7.2 - - - +
459A ALA 3.4 1.7 + - - +
460A MSE 1.3 80.6 - - - +
462A SER* 1.3 77.2 + - - +
473A CYS* 2.8 37.8 + - - +
475A PHE* 4.4 4.5 - - + -
522A LYS* 3.9 25.8 - - + +
525A LEU* 3.6 36.8 - - + +
526A ARG* 3.1 33.2 - - + +
529A ILE* 4.5 5.4 - - + -
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Residues in contact with SER 462 (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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431A ASP 5.7 1.3 + - - -
432A GLN 4.7 3.5 + - - -
433A ILE* 3.8 23.5 - - - +
461A VAL* 1.3 93.0 - - - +
463A MSE 1.3 62.3 + - - +
470A GLU* 3.3 31.1 + - - +
471A ARG 3.5 6.5 - - - -
526A ARG* 3.8 23.6 + - - +
529A ILE* 4.1 2.9 - - - +
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Residues in contact with MSE 463 (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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462A SER* 1.3 75.8 - - - +
464A PRO* 1.3 77.7 - - + +
470A GLU* 3.2 8.3 - - - -
471A ARG* 2.6 69.4 + - + +
472A SER 4.1 3.4 - - - +
473A CYS* 3.9 15.9 - - + -
504A ASP* 4.0 8.7 - - + -
505A ARG* 3.7 29.4 - - + -
529A ILE* 3.9 20.4 - - + -
533A LEU* 3.8 26.2 - - + -
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Residues in contact with PRO 464 (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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463A MSE 1.3 102.8 - - + +
465A ASP* 1.3 64.5 + - - +
469A GLY 3.9 7.9 - - - +
470A GLU* 5.1 1.1 - - + -
471A ARG* 4.2 0.7 - - - +
529A ILE* 5.3 0.2 - - + -
530A SER* 4.5 22.2 - - - +
533A LEU* 3.7 22.0 - - + +
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Residues in contact with ASP 465 (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 PRO* 1.3 80.6 - - - +
466A GLN* 1.3 57.2 + - - +
467A PHE* 2.7 39.2 + - - +
468A LEU 2.8 10.9 + - - +
469A GLY* 2.6 40.5 + - - +
470A GLU 4.1 9.0 - - - +
471A ARG* 2.5 46.6 + - - +
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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