Contacts of the helix formed by residues 388 - 401 (chain A) in PDB entry 2IZV
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 SER 388 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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387A PHE* 1.3 76.1 - - - +
389A LEU* 1.3 65.4 + - - +
390A GLN* 3.8 4.1 + - - +
391A HIS* 3.1 23.4 + - - +
392A ILE* 2.9 23.7 + - - +
418A TYR* 4.5 1.9 + - - -
76C TYR* 3.2 5.6 - - - -
112C CYS* 3.5 17.9 - - - -
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Residues in contact with LEU 389 (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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388A SER* 1.3 71.2 - - - +
390A GLN* 1.3 63.0 + - - +
392A ILE* 3.2 3.6 + - + +
393A CYS* 3.1 26.4 + - - -
72C LYS 5.2 0.4 - - - +
73C VAL* 4.1 26.2 - - + -
76C TYR* 3.3 40.3 + - + -
93C PHE* 3.9 26.7 - - + -
95C ILE* 4.1 14.1 - - + -
103C LEU* 4.2 14.1 - - + -
107C ALA* 3.7 18.2 - - + -
112C CYS* 2.8 26.0 + - - +
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Residues in contact with GLN 390 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
388A SER* 3.1 5.3 - - - +
389A LEU* 1.3 79.7 - - - +
391A HIS* 1.3 63.1 + - - +
393A CYS* 3.4 1.4 + - - -
394A ARG* 3.1 19.4 + - - +
415A MET* 3.2 24.9 - - - +
418A TYR* 3.5 37.1 - - + +
104C LEU* 3.6 25.8 - - + +
107C ALA* 3.6 9.3 - - + +
108C ASN* 3.3 32.5 + - - +
111C ASP* 5.9 0.9 - - - -
112C CYS 3.3 12.9 + - - +
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Residues in contact with HIS 391 (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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278A LEU* 5.8 0.4 - - + -
282A ASN* 2.6 36.9 + - + -
287A TYR* 5.1 0.9 - - - -
387A PHE* 3.8 21.3 - + + -
388A SER* 3.1 23.5 + - - +
390A GLN* 1.3 78.9 - - - +
392A ILE* 1.3 65.3 + - + +
394A ARG* 2.8 38.5 + - - +
395A THR* 3.1 32.7 + - + +
418A TYR* 3.2 11.1 + - - +
422A TYR* 4.1 13.9 - + - -
1432A CL 3.8 21.5 - - + +
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Residues in contact with ILE 392 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279A LEU* 6.3 0.7 - - + -
387A PHE* 4.0 28.9 - - + +
388A SER 2.9 20.1 + - - +
389A LEU* 3.2 5.6 + - - +
391A HIS* 1.3 78.0 - - + +
393A CYS* 1.3 60.0 + - - +
395A THR* 2.6 28.8 + - - +
396A VAL* 3.3 11.3 + - + +
76C TYR* 4.1 13.2 - - + -
79C TYR* 4.4 10.3 - - + +
93C PHE* 4.0 35.9 - - + +
95C ILE* 3.6 19.5 - - + -
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Residues in contact with CYS 393 (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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389A LEU* 3.1 18.1 + - - -
390A GLN 3.6 7.9 - - - +
392A ILE* 1.3 73.6 - - - +
394A ARG* 1.3 67.3 + - - +
396A VAL* 3.1 6.2 + - - +
397A ILE* 2.9 28.0 + - + +
95C ILE* 3.7 21.3 - - - -
100C ALA* 3.9 12.8 - - - +
103C LEU* 3.7 37.7 - - - -
104C LEU* 3.7 20.6 - - + -
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Residues in contact with ARG 394 (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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278A LEU* 5.1 2.0 - - - -
390A GLN 3.1 10.4 + - - +
391A HIS* 2.8 52.6 + - - +
393A CYS* 1.3 77.7 - - - +
395A THR* 1.3 58.5 + - - +
397A ILE 3.2 0.2 + - - -
398A CYS* 2.9 46.7 + - - -
418A TYR* 3.1 63.1 + - + -
419A LEU* 3.8 30.2 + - + -
421A GLU* 2.7 33.3 + - - +
422A TYR* 3.7 21.7 + - - -
104C LEU* 4.2 1.4 - - + +
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Residues in contact with THR 395 (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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278A LEU* 4.2 14.2 - - + +
279A LEU* 3.6 31.6 + - - +
282A ASN* 3.6 24.2 - - + +
391A HIS* 3.1 41.5 + - + +
392A ILE* 2.6 25.6 + - - +
394A ARG* 1.3 75.1 - - + +
396A VAL* 1.3 61.6 + - - +
398A CYS* 3.9 1.9 - - - +
399A ASN* 3.2 23.2 + - - +
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Residues in contact with VAL 396 (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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279A LEU* 4.5 16.6 - - + -
392A ILE* 3.6 14.6 - - + +
393A CYS* 3.1 9.3 + - - +
395A THR* 1.3 83.2 + - - +
397A ILE* 1.3 64.0 + - - +
399A ASN* 3.3 13.4 + - - +
400A CYS* 3.3 18.3 - - - -
93C PHE 5.6 0.9 - - - +
95C ILE* 3.9 39.5 - - + +
97C PRO* 4.3 14.8 - - + -
100C ALA* 4.2 17.9 - - + -
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Residues in contact with ILE 397 (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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393A CYS 2.9 23.9 + - - +
394A ARG 3.8 2.5 - - - +
396A VAL* 1.3 68.9 - - - +
398A CYS* 1.3 67.7 + - - +
400A CYS* 3.0 13.9 + - - +
401A THR* 3.2 18.5 + - + -
406A ILE* 5.7 0.4 - - + -
409A LEU* 4.3 13.0 - - + -
419A LEU* 4.1 23.3 - - + -
103B MET* 4.1 20.4 - - + -
100C ALA* 3.7 30.5 - - + +
101C LEU* 3.4 25.1 - - + -
104C LEU* 3.6 24.7 - - + -
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Residues in contact with CYS 398 (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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274A LEU* 3.7 30.5 - - + +
275A VAL 6.2 0.2 - - - +
278A LEU* 3.9 24.9 - - + -
394A ARG* 2.9 31.8 + - - +
395A THR 3.9 1.1 - - - +
397A ILE* 1.3 76.4 - - - +
399A ASN* 1.3 57.7 + - - +
401A THR* 3.1 25.5 - - - +
406A ILE* 4.7 1.3 - - - -
419A LEU* 3.2 34.8 - - - -
422A TYR* 6.2 0.2 - - - -
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Residues in contact with ASN 399 (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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276A PRO 4.7 9.5 - - - +
278A LEU* 6.4 1.3 - - - -
279A LEU* 3.3 38.1 + - + +
395A THR 3.2 19.0 + - - +
396A VAL* 3.5 7.7 + - - +
397A ILE 3.1 0.8 - - - -
398A CYS* 1.3 77.3 - - - +
400A CYS* 1.3 61.5 + - - +
401A THR 3.5 1.6 - - - +
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Residues in contact with CYS 400 (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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396A VAL* 3.3 17.3 - - - -
397A ILE 3.0 8.3 + - - +
399A ASN* 1.3 79.3 - - - +
401A THR* 1.3 58.8 + - - +
102B VAL 3.5 10.8 - - - +
103B MET* 3.6 38.7 - - + +
104B LYS 4.3 6.6 - - - +
97C PRO* 3.8 33.9 - - - -
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Residues in contact with THR 401 (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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274A LEU* 3.9 10.5 - - + +
397A ILE* 3.2 22.0 + - + +
398A CYS* 3.1 16.4 - - - +
399A ASN 3.5 1.4 - - - +
400A CYS* 1.3 80.7 + - - +
402A THR* 1.3 83.8 + - - +
405A GLY 3.9 6.4 - - - -
406A ILE* 3.6 20.5 - - + -
409A LEU* 4.8 2.1 - - + +
102B VAL* 3.2 33.0 + - - +
103B MET* 4.4 7.8 - - - +
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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