Contacts of the helix formed by residues 403 - 411 (chain A) in PDB entry 3IZ0
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 ALA 403 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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185A TYR* 4.1 1.8 - - - +
398A MET* 3.7 27.4 - - + +
401A LYS 2.8 8.9 + - - -
402A ARG* 1.3 89.9 - - - +
404A PHE* 1.3 73.1 + - + +
405A VAL* 2.7 8.3 + - - +
406A HIS 4.3 2.1 + - - -
261B PRO* 2.7 23.8 - - + +
262B PHE* 3.8 18.2 - - - -
346B TRP* 4.4 11.4 - - + -
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Residues in contact with PHE 404 (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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181A VAL* 3.4 29.2 - - + -
182A VAL* 3.3 29.8 - - + -
185A TYR* 4.1 11.0 - + + -
398A MET* 4.4 11.2 - - - -
402A ARG 3.1 0.2 + - - -
403A ALA* 1.3 92.5 - - + +
405A VAL* 1.3 61.6 + - - +
406A HIS* 3.4 2.0 - - - -
407A TRP* 3.5 23.6 + + + +
408A TYR* 3.3 18.4 - - + -
257B VAL* 4.1 13.5 - - + +
258B ASN* 3.5 21.8 - - - -
260B VAL 3.5 15.5 - - - -
261B PRO* 3.7 31.0 - - + -
314B THR* 4.1 5.2 - - - -
347B ILE* 4.2 10.1 - - + -
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Residues in contact with VAL 405 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185A TYR* 3.9 14.6 - - + +
399A TYR* 4.1 20.4 - - + -
402A ARG* 2.5 60.0 + - + +
403A ALA 2.7 4.0 + - - -
404A PHE* 1.3 67.8 - - - +
406A HIS* 1.3 51.9 + - - +
407A TRP 2.6 17.8 + - - -
408A TYR* 2.7 20.7 + - - +
409A VAL* 3.2 28.3 + - + +
415A GLU* 6.6 0.4 - - - -
418A PHE* 4.6 12.6 - - + -
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Residues in contact with HIS 406 (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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403A ALA 4.3 2.2 + - - -
405A VAL* 1.3 78.3 - - - +
407A TRP* 1.3 108.1 + + - +
408A TYR 3.3 0.4 - - - -
409A VAL* 4.2 10.5 - - - -
410A GLY* 3.5 17.5 + - - -
411A GLU* 5.4 0.3 - - - +
260B VAL* 3.4 18.0 - - + +
261B PRO 3.9 6.6 + - - -
263B PRO* 3.7 49.4 - - + +
170C TYR 5.7 2.7 - - - +
171C THR* 5.2 7.0 - - + -
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Residues in contact with TRP 407 (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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102A ASN* 3.1 9.2 + - - +
404A PHE* 3.5 24.2 + - + +
405A VAL 2.6 5.7 + - - -
406A HIS* 1.3 106.0 - + - +
408A TYR* 1.3 52.4 + - + +
411A GLU* 2.6 43.7 - - - +
165B ILE* 5.6 3.8 - - + -
199B ASP* 4.5 16.4 - - + -
253B ARG* 5.6 8.1 - - + -
256B ALA* 3.6 24.8 + - + -
257B VAL* 3.6 42.8 - - + -
260B VAL* 2.8 44.6 + - + +
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Residues in contact with TYR 408 (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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102A ASN* 3.1 17.1 - - + -
103A TYR* 3.1 28.9 - - + -
104A ALA* 3.1 34.9 - - + +
182A VAL* 3.8 9.7 - - + +
185A TYR* 3.1 37.4 - + + +
186A ASN* 3.0 21.9 + - - -
189A LEU* 5.1 0.2 - - + -
404A PHE* 3.3 28.7 - - + -
405A VAL* 2.7 6.1 + - - +
407A TRP* 1.3 79.7 - - + +
409A VAL* 1.3 57.1 + - - +
410A GLY 3.1 1.3 - - - -
411A GLU* 2.4 35.3 + - - +
412A GLY 3.5 0.2 + - - -
413A MET* 3.8 5.0 - - + +
418A PHE* 3.1 36.1 - + + -
257B VAL* 5.9 0.4 - - + -
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Residues in contact with VAL 409 (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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405A VAL* 3.2 39.3 - - + +
406A HIS* 4.2 6.3 - - - +
408A TYR* 1.3 74.8 - - + +
410A GLY* 1.3 55.1 + - - +
411A GLU 2.6 12.0 + - - -
412A GLY* 3.0 11.4 + - - -
413A MET* 3.7 23.4 + - - +
414A GLU* 5.1 10.3 - - - -
415A GLU 5.8 0.9 - - - +
418A PHE* 5.5 2.7 - - + -
122C VAL* 6.1 6.1 - - + -
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Residues in contact with GLY 410 (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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109A THR* 5.0 0.3 + - - -
406A HIS 3.5 14.4 + - - -
408A TYR 3.1 0.8 - - - -
409A VAL* 1.3 78.1 - - - +
411A GLU* 1.3 77.2 + - - +
412A GLY 3.7 0.9 - - - -
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Residues in contact with GLU 411 (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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102A ASN* 3.7 9.2 - - - +
104A ALA* 3.9 4.3 - - + +
105A ARG* 3.7 48.3 + - + +
108A TYR* 3.7 11.3 - - - +
109A THR* 3.4 25.6 + - - +
406A HIS 5.4 0.2 - - - +
407A TRP* 2.6 40.0 - - - +
408A TYR 2.4 28.8 + - - +
409A VAL 2.6 1.8 + - - -
410A GLY* 1.3 90.2 - - - +
412A GLY* 1.3 61.3 + - - +
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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