Contacts of the strand formed by residues 433 - 438 (chain C) in PDB entry 1ZM9
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 ARG 433 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68C ILE* 4.8 11.7 - - - +
390C ASP* 4.3 12.1 + - - -
395C TYR* 4.1 17.3 + - - -
407C SER* 3.5 10.1 - - - +
431C ILE* 3.4 3.8 + - - +
432C GLN* 1.3 117.0 + - - +
434C VAL* 1.3 64.8 + - - +
435C VAL* 4.1 10.0 - - + +
444C PRO* 5.3 16.9 - - + +
456C LEU* 3.6 1.9 - - - -
457C VAL* 2.7 54.5 + - + +
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Residues in contact with VAL 434 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
405C VAL* 4.3 15.7 - - + -
406C LYS* 3.7 13.5 - - - +
407C SER* 3.0 32.3 + - - +
431C ILE* 4.2 10.3 - - + -
433C ARG* 1.3 75.1 - - - +
435C VAL* 1.3 69.9 + - - +
444C PRO* 3.5 1.9 - - - +
445C ILE* 2.9 45.5 + - + +
446C ASP 3.9 2.9 - - - +
447C ASP 5.1 0.2 - - - -
448C CYS* 4.6 4.5 - - + -
454C ILE* 3.5 26.7 - - + -
455C GLY 3.6 5.2 - - - +
456C LEU* 4.3 1.8 - - + -
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Residues in contact with VAL 435 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
395C TYR* 4.3 5.6 - - + -
433C ARG* 4.6 7.6 - - + +
434C VAL* 1.3 82.8 - - - +
436C LEU* 1.3 59.4 + - - +
437C MET* 4.5 3.6 - - - -
442C VAL* 3.7 37.0 - - + -
443C GLU 3.4 7.0 - - - +
444C PRO* 3.9 21.1 - - + -
445C ILE* 4.1 1.1 - - - -
454C ILE* 3.0 7.9 - - - +
455C GLY* 2.9 46.7 + - - +
457C VAL* 4.0 27.1 - - + -
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Residues in contact with LEU 436 (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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6C VAL* 5.7 6.5 - - + +
9C MET* 3.6 44.4 - - + -
13C MET* 3.5 30.1 - - + -
435C VAL* 1.3 71.9 - - - +
437C MET* 1.3 61.4 + - - +
438C MET* 3.0 27.1 + - + +
442C VAL* 3.1 22.7 - - - -
443C GLU* 2.9 25.0 + - + +
444C PRO 5.9 0.2 - - - +
445C ILE* 4.2 14.1 - - + -
453C ILE 5.1 2.0 - - - +
454C ILE* 3.4 22.7 - - + -
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Residues in contact with MET 437 (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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70C ILE* 3.9 24.2 - - + -
73C THR* 5.2 4.7 - - - +
74C ALA* 3.0 20.4 - - + +
76C SER* 4.9 4.6 + - - -
386C VAL* 3.3 34.5 - - + -
395C TYR* 4.6 9.9 - - + -
396C ALA 4.7 2.7 - - - +
397C PHE* 3.6 41.3 - - + -
435C VAL* 3.8 4.2 + - - -
436C LEU* 1.3 69.6 - - - +
438C MET* 1.3 51.9 + - - +
439C GLY 2.6 20.0 + - - +
441C PHE 3.9 2.5 - - - -
442C VAL* 4.5 8.7 - - - -
453C ILE* 5.3 4.5 + - + -
454C ILE* 4.3 3.2 - - - +
455C GLY* 4.0 24.8 - - - +
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Residues in contact with MET 438 (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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4C PHE* 5.5 1.1 - - + +
9C MET* 3.8 42.8 - - + -
45C ILE* 4.6 16.6 - - + +
46C ILE 4.7 0.4 - - - -
47C SER* 3.9 37.2 - - - +
75C ILE* 5.5 1.1 - - - -
76C SER* 4.0 17.7 - - - +
436C LEU* 3.0 25.5 + - + +
437C MET* 1.3 66.3 - - - +
439C GLY* 1.3 58.2 + - - +
440C ARG 2.9 9.4 + - - -
441C PHE* 2.9 33.6 + - + +
443C GLU* 4.3 13.7 - - + +
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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