Contacts of the helix formed by residues 374 - 389 (chain A) in PDB entry 1IEQ
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 LYS 374 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133A LEU* 4.8 4.2 - - - +
370A GLU 3.9 11.9 - - - +
371A GLN* 3.0 52.5 + - - +
372A LEU 3.2 1.8 + - - -
373A GLY* 1.3 78.0 - - - +
375A GLN* 1.3 60.8 + - - +
376A GLU* 3.2 34.5 - - - +
377A HIS* 2.8 51.7 + - + +
378A ARG 3.4 3.1 + - - -
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Residues in contact with GLN 375 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
373A GLY 3.2 4.7 + - - +
374A LYS* 1.3 73.8 - - - +
376A GLU* 1.3 62.7 + - - +
378A ARG* 3.1 29.4 + - - +
379A ASP* 2.8 57.7 + - - +
382A ARG* 6.1 0.6 - - - +
549A GLU* 5.1 2.4 + - - -
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Residues in contact with GLU 376 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
374A LYS* 3.0 37.2 + - - +
375A GLN* 1.3 79.4 + - - +
377A HIS* 1.3 59.9 + - + +
379A ASP* 3.2 14.7 + - - +
380A LEU* 2.9 26.0 + - - +
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Residues in contact with HIS 377 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107A THR* 3.5 7.9 - - + +
109A PHE* 3.7 4.6 - - + -
130A ALA* 3.8 28.7 + - + +
133A LEU* 4.1 12.8 - - + +
134A GLU* 2.9 37.6 - - + +
371A GLN* 3.3 35.0 + - - -
374A LYS* 2.8 36.9 + - + +
376A GLU* 1.3 79.6 - - + +
378A ARG* 1.3 59.0 + - - +
380A LEU* 3.0 10.7 + - - +
381A ALA* 2.8 28.1 + - - +
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Residues in contact with ARG 378 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105A GLY* 3.1 28.7 + - - -
106A ALA 4.5 0.6 + - - -
107A THR* 3.7 24.3 - - + +
373A GLY* 3.3 21.1 + - - -
374A LYS 3.4 4.0 + - - +
375A GLN* 3.1 34.9 + - - +
377A HIS* 1.3 78.1 - - - +
379A ASP* 1.3 58.1 + - - +
381A ALA 3.3 0.5 + - - -
382A ARG* 2.8 29.7 + - - +
443A VAL* 3.4 47.4 + - - +
444A GLY* 4.6 0.8 - - - -
548A SER* 3.9 5.3 + - - -
549A GLU* 2.9 43.9 + - - +
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Residues in contact with ASP 379 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
375A GLN* 2.8 42.0 + - - +
376A GLU* 3.4 18.1 - - - +
378A ARG* 1.3 73.8 - - - +
380A LEU* 1.3 61.9 + - - +
382A ARG* 3.2 19.9 + - - +
383A GLU* 2.9 27.3 + - - +
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Residues in contact with LEU 380 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109A PHE* 3.8 11.7 - - + -
123A LEU* 3.6 19.1 - - + -
126A ARG* 3.5 69.1 - - + +
127A ILE* 3.7 13.5 - - + -
130A ALA* 4.0 10.8 - - + -
376A GLU 2.9 12.3 + - - +
377A HIS* 3.2 8.3 - - - +
379A ASP* 1.3 76.4 - - - +
381A ALA* 1.3 58.6 + - - +
383A GLU* 2.9 11.0 + - - +
384A ALA* 2.8 25.6 + - - +
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Residues in contact with ALA 381 (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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107A THR* 3.9 9.6 - - + -
108A ILE 4.3 9.6 - - - +
109A PHE* 3.6 27.6 - - + -
110A PRO* 4.2 3.1 - - + +
377A HIS 2.8 12.9 + - - +
378A ARG 3.5 7.4 - - - +
380A LEU* 1.3 75.7 - - - +
382A ARG* 1.3 54.9 + - - +
384A ALA* 3.2 4.3 + - - +
385A ALA* 2.7 36.4 + - - +
546A PRO 5.0 0.4 - - - +
549A GLU* 3.7 16.6 - - + -
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Residues in contact with ARG 382 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
375A GLN* 6.1 0.6 - - - +
378A ARG 2.8 14.2 + - - +
379A ASP* 3.3 22.4 + - - +
380A LEU 3.1 0.2 - - - -
381A ALA* 1.3 78.1 - - - +
383A GLU* 1.3 61.9 + - - +
385A ALA* 3.3 2.9 + - - -
386A ARG* 3.0 23.7 + - - +
549A GLU* 4.0 15.3 - - + -
551A GLN* 3.1 46.3 + - + +
552A GLY* 3.6 13.1 - - - +
555A ASP* 2.9 39.0 + - - +
560A ASP* 5.6 1.0 + - - -
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Residues in contact with GLU 383 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123A LEU* 3.6 9.0 - - + +
126A ARG* 2.8 35.0 + - - -
379A ASP 2.9 11.7 + - - +
380A LEU* 2.9 11.4 + - - +
382A ARG* 1.3 78.3 - - - +
384A ALA* 1.3 56.6 + - - +
386A ARG* 3.4 21.8 + - - +
387A LYS* 2.8 71.7 + - + +
555A ASP* 6.0 0.2 - - - -
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Residues in contact with ALA 384 (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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110A PRO* 3.9 13.1 - - + +
115A LEU* 4.2 4.0 - - + +
118A THR* 4.1 1.7 - - - +
123A LEU* 3.8 27.8 - - + +
127A ILE* 4.0 22.9 - - + -
380A LEU 2.8 12.7 + - - +
381A ALA* 3.7 7.2 - - - +
383A GLU* 1.3 73.1 - - - +
385A ALA* 1.3 65.6 + - - +
387A LYS* 3.7 1.1 - - - +
388A SER* 2.9 27.2 + - - -
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Residues in contact with ALA 385 (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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110A PRO* 3.7 9.6 - - - +
381A ALA 2.7 21.4 + - - +
382A ARG 3.6 4.5 - - - +
384A ALA* 1.3 72.2 - - - +
386A ARG* 1.3 62.8 + - - +
388A SER* 2.8 19.2 + - - -
389A LEU* 3.2 17.2 - - - +
546A PRO* 4.0 24.7 - - + +
549A GLU* 4.0 12.8 - - + +
552A GLY* 4.0 14.6 - - - -
553A VAL* 4.9 1.1 - - + +
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Residues in contact with ARG 386 (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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382A ARG 3.0 15.1 + - - +
383A GLU* 3.6 28.4 + - - +
385A ALA* 1.3 77.1 - - - +
387A LYS* 1.3 87.2 + - - +
388A SER 3.1 1.2 + - - -
389A LEU* 3.2 22.3 + - - +
552A GLY* 3.4 24.7 + - - +
555A ASP* 4.1 15.6 + - + +
556A ALA* 4.4 11.8 - - + +
561A PHE* 3.4 58.2 - - + +
562A GLY 4.7 9.3 + - - -
563A PHE* 5.6 2.7 - - - +
564A THR* 5.3 8.6 + - - +
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Residues in contact with LYS 387 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118A THR* 3.5 25.8 - - + +
120A ASP* 3.2 26.6 + - + +
123A LEU* 4.0 14.5 - - + +
126A ARG* 5.0 1.6 - - - +
383A GLU* 2.8 52.5 + - - +
384A ALA* 4.0 2.2 - - - +
385A ALA 3.4 0.2 - - - -
386A ARG* 1.3 100.5 - - - +
388A SER* 1.3 59.3 + - - +
389A LEU 3.4 0.7 - - - -
564A THR* 4.3 16.0 + - - +
565A GLY* 3.6 20.4 + - - -
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Residues in contact with SER 388 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110A PRO* 4.5 7.9 - - - +
114A GLY* 3.0 37.2 - - - -
115A LEU* 5.0 0.2 - - - -
117A ALA* 3.5 10.3 - - - +
118A THR* 3.6 3.4 - - - -
384A ALA 2.9 15.6 + - - -
385A ALA* 2.8 22.0 + - - -
386A ARG 3.1 0.2 - - - -
387A LYS* 1.3 76.1 - - - +
389A LEU* 1.3 65.5 + - - +
543A ALA 4.5 6.1 + - - -
544A TRP* 3.0 28.8 + - - -
546A PRO* 5.3 1.4 - - - +
565A GLY* 4.8 0.2 - - - -
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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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385A ALA 3.2 17.3 - - - +
386A ARG 3.2 10.8 + - - +
387A LYS 4.3 0.2 - - - +
388A SER* 1.3 77.4 + - - +
390A VAL* 1.3 59.0 + - - +
391A LEU 4.1 1.1 + - - -
541A VAL* 3.8 13.7 - - + -
542A ALA 3.5 3.4 - - - -
543A ALA* 3.6 35.7 - - + +
546A PRO* 5.1 1.8 - - + -
552A GLY 3.7 17.7 - - - +
553A VAL* 3.8 23.8 - - + +
556A ALA* 3.7 29.6 - - + -
557A LEU* 6.1 0.2 - - + -
563A PHE* 4.1 16.1 - - + +
564A THR 4.7 0.3 + - - -
565A GLY* 3.3 24.3 + - - -
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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