Contacts of the helix formed by residues 399 - 408 (chain A) in PDB entry 2JIF
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 PRO 399 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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311A TYR* 3.5 51.6 - - + +
397A ASP 4.8 0.7 - - - +
398A TYR* 1.4 87.0 - - + +
400A VAL* 1.3 64.7 + - + +
401A GLU 3.4 0.9 - - - -
402A LYS* 3.4 17.0 + - + +
403A TYR* 3.3 17.4 + - + -
1435A EDO 3.4 30.7 - - - -
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Residues in contact with VAL 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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308A CYS* 3.6 22.7 - - - +
311A TYR* 3.8 30.3 - - + -
312A THR* 3.8 12.3 - - - +
382A THR 4.2 1.1 - - - +
385A CYS* 3.7 3.6 - - + -
386A ILE* 3.7 35.4 - - + +
389A MET* 4.1 15.9 - - + -
393A GLY* 4.6 6.5 - - - +
398A TYR* 3.4 2.9 - - + +
399A PRO* 1.3 77.2 - - + +
401A GLU* 1.3 66.4 + - - +
403A TYR* 3.3 10.6 + - + +
404A PHE* 3.1 20.6 + - - +
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Residues in contact with GLU 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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84A ASP* 4.8 0.3 - - - +
386A ILE* 4.2 8.5 - - - -
393A GLY 3.6 18.1 + - - +
394A TYR 4.7 0.2 - - - -
395A THR 3.5 26.2 - - - +
396A LYS* 2.8 44.6 + - + +
398A TYR 4.1 4.0 + - - +
400A VAL* 1.3 77.6 - - - +
402A LYS* 1.3 64.3 + - - +
404A PHE* 3.4 3.1 + - - +
405A ARG* 2.8 62.2 + - - +
253C LEU* 3.7 27.5 - - + +
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Residues in contact with LYS 402 (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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80A VAL* 3.5 30.7 - - + +
81A SER* 5.5 1.3 - - - -
84A ASP* 3.7 32.3 - - + +
131A VAL 4.8 1.0 + - - -
132A ASP* 2.9 32.2 + - - +
134A SER* 5.0 3.3 + - - -
256A ARG 6.2 1.1 - - - +
257A ALA* 6.5 0.4 - - - -
399A PRO* 3.4 11.7 + - + +
400A VAL 3.2 0.6 - - - -
401A GLU* 1.3 82.9 + - - +
403A TYR* 1.3 68.9 + - - +
405A ARG* 3.2 24.5 + - - +
406A ASP* 2.8 60.5 + - - +
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Residues in contact with TYR 403 (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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129A ALA 4.0 10.8 - - - -
130A LYS 2.7 28.8 + - - -
131A VAL 4.4 6.5 - - - -
132A ASP* 5.7 1.1 - - - -
133A ALA* 6.0 1.1 - - + -
304A LEU* 3.5 31.8 - - + +
307A GLY 3.9 5.9 + - - -
308A CYS* 3.5 35.4 - - + -
311A TYR* 5.1 2.2 - - + -
382A THR* 3.8 16.8 - - + -
399A PRO* 3.3 25.6 + - + -
400A VAL* 3.3 8.9 + - + +
402A LYS* 1.3 79.6 - - + +
404A PHE* 1.3 57.4 + - - +
406A ASP* 4.4 7.0 - - - -
407A ALA* 2.9 32.7 + - - +
1435A EDO 3.0 36.7 + - - -
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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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379A GLY* 4.8 1.8 - - - -
382A THR* 3.5 16.4 + - - -
383A SER* 3.8 32.1 - - - -
386A ILE* 3.5 24.0 - - + -
400A VAL 3.1 8.4 + - - +
401A GLU 3.5 8.3 - - - +
402A LYS 3.2 0.2 - - - -
403A TYR* 1.3 79.0 - - - +
405A ARG* 1.3 64.5 + - + +
407A ALA* 3.5 8.5 + - - +
408A LYS* 3.6 12.0 + - - +
253C LEU* 3.9 26.5 - - + -
404C PHE* 3.3 50.0 - + - -
405C ARG* 5.0 0.4 - - - -
408C LYS* 3.7 30.5 - - + -
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Residues in contact with ARG 405 (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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84A ASP* 3.1 38.8 + - - -
253A LEU* 3.0 54.0 + - + +
254A GLY* 3.8 5.2 - - - -
256A ARG* 3.6 10.1 - - - +
396A LYS* 3.4 12.6 - - - +
401A GLU* 2.8 48.3 + - - +
402A LYS* 3.2 17.0 + - - +
404A PHE* 1.3 77.7 - - + +
406A ASP* 1.3 57.1 + - - +
407A ALA 3.6 0.2 + - - -
408A LYS* 3.6 4.9 + - - +
253C LEU* 3.5 25.1 - - + -
394C TYR* 2.7 32.7 + - - -
396C LYS* 6.0 0.7 - - - +
404C PHE* 5.1 0.4 - - - -
405C ARG* 4.2 5.2 - - + +
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Residues in contact with ASP 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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84A ASP* 4.9 1.4 - - - +
132A ASP* 4.3 0.5 - - - +
133A ALA* 4.0 26.8 + - + +
134A SER* 5.1 0.7 - - - -
254A GLY* 3.5 4.3 - - - -
255A LEU* 2.8 32.5 + - + +
256A ARG 4.6 0.5 + - - -
301A MET* 4.0 2.6 - - - +
304A LEU* 4.2 4.9 - - + +
402A LYS* 2.8 57.6 + - - +
403A TYR* 3.8 8.2 + - + +
405A ARG* 1.3 74.8 - - - +
407A ALA* 1.3 63.5 + - - +
408A LYS 3.2 0.5 + - - -
409A ILE* 3.1 26.7 + - - +
394C TYR* 3.7 4.7 - - - -
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Residues in contact with ALA 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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301A MET* 3.5 10.0 - - - +
304A LEU* 3.8 21.5 - - + -
375A SER 4.6 4.9 - - - +
378A ALA* 3.7 32.3 - - + +
379A GLY* 4.1 4.6 + - - +
382A THR* 3.7 7.4 - - - +
403A TYR 2.9 19.1 + - - +
404A PHE 3.9 2.9 - - - +
405A ARG 3.4 0.8 - - - -
406A ASP* 1.3 77.2 - - - +
408A LYS* 1.3 62.6 + - - +
410A GLY* 3.1 13.4 + - - -
411A THR* 4.5 1.9 + - - +
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Residues in contact with LYS 408 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
253A LEU* 4.2 3.6 - - + -
379A GLY* 5.7 3.9 - - - -
404A PHE 3.6 4.4 + - - +
405A ARG 3.9 11.0 - - - +
406A ASP 3.2 1.4 - - - -
407A ALA* 1.3 78.3 - - - +
409A ILE* 1.3 61.8 + - - +
410A GLY 3.2 0.7 + - - -
411A THR* 3.5 39.0 + - - +
412A ILE* 4.0 5.2 - - - +
383C SER* 2.7 34.2 + - - +
386C ILE* 4.0 30.5 - - + -
387C GLU* 2.6 30.2 + - - -
394C TYR* 4.0 6.1 - - + -
404C PHE* 3.6 35.9 - - + -
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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