Contacts of the strand formed by residues 423 - 428 (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 ILE 423 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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330A PHE* 3.9 29.4 - - + -
336A LEU* 5.1 3.6 - - + -
338A ASN* 4.1 18.2 - - - +
352A THR* 4.5 0.2 - - - -
353A GLN* 2.7 37.5 + - - +
354A GLY 2.5 19.0 + - - +
356A PRO* 4.9 6.7 - - + -
363A SER* 5.2 4.0 - - - +
381A LEU* 4.2 19.1 - - + -
415A VAL* 3.6 32.3 - - + -
416A ARG 4.1 3.4 - - - +
417A LEU* 3.4 25.6 - - + -
421A GLY 3.9 4.0 - - - +
422A TYR* 1.3 72.5 - - - +
424A VAL* 1.3 58.5 + - - +
425A VAL* 3.9 4.0 - - + -
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Residues in contact with VAL 424 (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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309A LYS* 4.2 8.3 - - - +
351A ASN 3.6 25.6 - - - +
352A THR* 4.1 13.9 - - + -
353A GLN* 3.6 8.5 - - - +
415A VAL* 3.8 0.7 - - - -
416A ARG* 3.4 72.4 + - - +
418A THR* 4.9 6.7 - - - -
422A TYR 4.7 4.5 - - - +
423A ILE* 1.3 80.1 - - - +
425A VAL* 1.3 66.3 + - - +
426A GLU* 3.7 1.7 + - - +
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Residues in contact with VAL 425 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
309A LYS* 2.6 40.0 + - + +
330A PHE* 3.5 37.2 - - + -
353A GLN* 3.3 27.1 - - + +
413A ASP* 4.7 6.1 - - + -
414A ILE 4.0 5.4 - - - +
415A VAL* 3.7 13.5 - - + -
423A ILE* 3.9 1.1 - - + -
424A VAL* 1.3 73.7 - - - +
426A GLU* 1.3 57.9 + - - +
427A GLY* 3.3 20.4 - - - +
600A AMP 3.5 26.5 - - + +
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Residues in contact with GLU 426 (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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309A LYS* 4.4 6.8 - - - +
378A THR* 3.4 12.9 - - + +
414A ILE* 3.0 25.8 + - + +
415A VAL* 5.2 0.4 - - - -
424A VAL 3.7 1.9 + - - +
425A VAL* 1.3 74.4 - - - +
427A GLY* 1.3 61.7 + - - +
432A GLN* 3.0 19.6 - - - +
439A LYS* 2.8 43.0 + - - -
441A ALA* 3.8 26.2 - - + +
442A ALA 5.5 0.7 + - - -
443A GLU* 3.4 29.3 + - - +
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Residues in contact with GLY 427 (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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309A LYS* 6.2 1.1 - - - -
413A ASP* 3.7 3.6 - - - +
414A ILE* 2.8 33.4 + - - +
425A VAL* 3.3 14.0 - - - +
426A GLU* 1.3 84.2 - - - +
428A ARG* 1.3 60.8 + - - -
429A ALA 3.7 0.2 + - - -
431A ASP* 5.4 2.7 - - - -
600A AMP 5.6 3.8 - - - -
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Residues in contact with ARG 428 (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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191A GLY* 5.2 0.6 - - - -
192A GLY 5.1 4.0 - - - +
193A SER 5.3 8.7 + - - +
307A GLY 4.9 0.2 + - - -
412A GLY 3.9 8.7 - - - +
413A ASP* 4.3 1.6 - - - +
414A ILE* 5.0 0.2 - - - -
427A GLY* 1.3 72.5 - - - -
429A ALA* 1.3 56.6 + - - +
430A LYS* 4.2 6.3 - - + +
431A ASP* 2.5 60.1 + - - +
432A GLN* 3.4 3.5 + - - +
519A LYS* 3.8 5.3 - - - +
600A AMP 2.2 89.2 + - - +
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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