Contacts of the strand formed by residues 419 - 426 (chain I) in PDB entry 1DZH
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 419 (chain I).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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52I SER* 3.9 12.3 - - - +
55I ASN* 6.0 4.0 - - - +
56I SER* 5.0 1.6 - - - -
81I LEU* 4.2 16.3 - - - +
126I LEU* 3.7 23.6 - - + -
130I LEU* 4.5 1.4 - - - +
413I ARG* 3.2 5.7 - - - +
414I GLU* 2.8 40.6 + - - +
417I LEU* 3.2 34.5 - - + +
418I ASN* 1.3 78.0 - - - +
420I ILE* 1.3 69.1 + - - +
421I ILE* 4.2 5.4 - - - +
805I GOL 5.2 0.4 - - - -
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Residues in contact with ILE 420 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55I ASN 6.4 0.2 - - - -
56I SER* 3.5 29.3 + - - +
59I ALA* 4.4 15.5 - - + -
60I THR* 5.4 3.6 - - - +
80I PRO* 4.3 12.0 - - + +
81I LEU* 3.6 20.4 + - - +
304I LEU* 4.5 4.0 - - + -
411I PHE* 3.8 34.3 - - + -
412I ILE 4.2 2.5 - - - +
413I ARG* 4.3 4.0 - - + +
419I THR* 1.3 73.2 + - - +
421I ILE* 1.3 62.0 + - - +
422I PHE 3.6 26.7 - - - +
423I MET* 4.3 3.4 - - + -
805I GOL 3.9 25.6 - - - +
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Residues in contact with ILE 421 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79I SER* 2.9 31.8 + - - +
80I PRO* 3.5 3.5 - - - +
81I LEU* 4.2 13.4 + - + -
130I LEU* 4.4 2.9 - - + -
140I LEU* 3.6 40.2 - - + -
219I ILE* 4.3 9.4 - - + -
279I ILE* 4.3 13.2 - - + -
412I ILE* 2.7 24.4 + - + +
413I ARG 4.8 0.7 - - - -
414I GLU* 3.9 30.5 - - + +
419I THR* 3.4 8.2 + - - +
420I ILE* 1.3 74.8 - - - +
422I PHE* 1.3 82.5 + - + +
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Residues in contact with PHE 422 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77I PHE* 3.4 40.2 - + + -
78I LEU 3.5 4.9 - - - +
79I SER* 3.6 27.1 - - - -
80I PRO* 3.9 0.7 - - - -
219I ILE* 3.2 35.9 - - + -
221I PHE* 3.8 31.9 - + + -
371I ALA* 4.3 9.6 - - + -
372I PHE 4.7 6.1 - - - -
373I LEU* 6.1 0.7 - - + -
410I VAL 4.6 0.2 - - - -
411I PHE* 3.5 2.8 - - - -
412I ILE* 2.9 46.3 + - + -
420I ILE* 3.6 7.8 - - - +
421I ILE* 1.3 97.2 - - + +
423I MET* 1.3 60.9 + - - +
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Residues in contact with MET 423 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59I ALA* 3.4 41.3 - - - +
60I THR* 4.8 3.1 - - - +
63I TYR* 3.5 39.7 - - + -
77I PHE* 3.5 8.2 - - - -
78I LEU* 3.0 39.7 + - + +
80I PRO* 3.6 16.8 - - + -
299I LEU* 4.4 7.0 - - + -
409I LEU* 5.8 1.6 - - + -
410I VAL 3.3 4.9 - - - -
411I PHE* 3.5 39.5 - - + -
420I ILE* 4.3 2.5 - - + -
422I PHE* 1.3 74.6 - - - +
424I GLY* 1.3 60.0 + - - +
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Residues in contact with GLY 424 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63I TYR* 4.1 10.6 - - - -
76I ILE 3.2 15.5 - - - -
77I PHE* 4.0 7.2 - - - -
409I LEU* 3.3 13.7 - - - +
410I VAL* 2.9 34.9 + - - -
423I MET* 1.3 78.6 - - - +
425I ARG* 1.3 60.6 + - - -
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Residues in contact with ARG 425 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63I TYR* 3.3 12.6 - - - +
67I ALA* 3.7 18.0 + - - +
70I LYS* 4.9 4.8 + - - +
71I ASN 3.8 10.1 + - - -
72I ASP* 3.5 19.3 + - - +
74I ASP* 3.0 25.3 + - - +
75I ASN* 3.4 6.4 - - - -
76I ILE* 2.9 59.3 + - + +
292I LEU* 3.4 28.4 - - + +
296I GLU* 2.6 40.4 + - - +
325I ILE* 3.5 7.7 - - - +
408I PHE 3.8 3.8 - - - +
409I LEU* 4.7 1.3 - - + +
410I VAL* 4.6 0.6 - - - +
424I GLY* 1.3 72.1 - - - -
426I VAL* 1.3 68.6 + - - +
427I ALA* 3.9 10.5 - - - -
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Residues in contact with VAL 426 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75I ASN* 3.5 4.3 - - - +
239I PHE* 3.9 1.8 - - + -
323I PHE* 3.8 28.9 - - + -
325I ILE* 4.2 7.6 - - + -
407I PRO* 3.0 23.0 - - - +
408I PHE* 3.0 43.1 + - + -
410I VAL* 3.6 23.3 - - + -
425I ARG* 1.3 76.9 - - - +
427I ALA* 1.3 60.4 + - - +
428I ASN 4.4 0.9 - - - +
429I PRO* 3.9 32.5 - - + -
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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