Contacts of the helix formed by residues 318 - 323 (chain C) in PDB entry 1IZO
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 LEU 318 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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290C GLY* 3.3 23.3 - - - +
291C PRO 3.0 12.1 + - - +
292C PHE 3.8 11.2 - - - +
293C LEU* 3.7 37.7 - - + -
316C LEU* 3.1 19.0 + - + +
317C ASP* 1.3 72.3 + - - +
319C TYR* 1.3 71.0 + - - +
321C THR* 3.4 3.6 + - - -
322C ASN* 3.1 28.6 + - - +
350C ILE* 3.5 38.8 - - + +
351C PRO* 4.6 2.0 - - + +
501C HEM 3.9 21.1 - - + -
2601C PAM 5.7 0.4 - - + -
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Residues in contact with TYR 319 (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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22C TYR* 3.3 37.5 - + + +
23C LEU* 3.5 19.5 - - + -
26C LYS* 5.0 10.8 - - + -
286C TYR 4.6 1.7 + - - -
287C TYR 4.9 0.7 - - - -
288C PRO* 3.6 42.6 - - + +
290C GLY 4.2 3.2 + - - +
291C PRO* 3.4 6.2 + - + +
317C ASP* 3.1 3.5 + - - +
318C LEU* 1.3 77.7 - - - +
320C GLY* 1.3 61.7 + - - +
322C ASN* 2.8 25.3 + - - +
323C HIS* 3.0 56.9 + + - -
397C LEU* 3.4 25.7 - - + +
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Residues in contact with GLY 320 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26C LYS* 4.3 23.7 - - - +
50C THR* 3.9 6.3 - - - -
317C ASP* 2.6 28.8 + - - -
319C TYR* 1.3 76.6 - - - +
321C THR* 1.3 55.3 + - - -
323C HIS* 2.8 20.4 + - - +
324C ASP* 3.0 13.6 + - - +
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Residues in contact with THR 321 (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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50C THR* 3.3 6.2 + - - -
51C GLY* 3.2 20.6 + - - +
52C ALA* 3.8 23.3 - - + +
316C LEU* 4.9 1.0 - - - +
317C ASP 2.7 25.7 + - - -
318C LEU 3.4 4.9 + - - -
319C TYR 3.2 0.6 - - - -
320C GLY* 1.3 74.4 - - - +
322C ASN* 1.3 61.6 + - - +
323C HIS 3.0 0.7 + - - -
324C ASP* 3.2 21.7 + - + +
327C LEU* 5.9 1.5 - - + +
328C TRP* 3.8 7.4 - - - -
347C PHE 3.9 16.4 - - - +
348C ASP 3.8 7.6 - - - +
350C ILE* 4.2 18.4 - - + +
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Residues in contact with ASN 322 (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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284C ARG 4.5 1.2 + - - -
285C ARG* 3.4 48.4 + - + +
287C TYR 5.9 0.6 + - - -
290C GLY 5.6 1.0 + - - -
318C LEU* 3.1 19.4 + - - +
319C TYR* 2.8 12.8 + - - +
321C THR* 1.3 75.6 - - - +
323C HIS* 1.3 62.0 + - + +
324C ASP 3.5 0.7 - - - -
328C TRP* 3.5 12.9 - - - +
348C ASP 4.7 0.2 - - - -
349C MET* 3.5 8.2 - - - -
350C ILE* 2.8 30.0 + - - +
351C PRO* 3.5 33.5 - - - +
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Residues in contact with HIS 323 (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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26C LYS* 3.6 29.1 + - + +
285C ARG* 3.3 18.8 + - - -
286C TYR* 2.9 37.1 + + - -
287C TYR 5.3 0.4 - - - -
319C TYR* 3.0 58.1 + + + +
320C GLY* 2.8 12.4 + - - +
322C ASN* 1.3 80.2 - - + +
324C ASP* 1.3 58.1 + - - +
325C PRO* 3.5 9.0 - - - +
331C PRO* 3.4 36.9 - - + +
332C ASP* 3.9 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