Contacts of the helix formed by residues 421 - 431 (chain D) in PDB entry 2J2M
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 PHE 421 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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171D PRO* 3.7 20.2 - - + -
174D THR* 3.7 12.6 - - + -
419D ASN 3.2 0.2 - - - -
420D ASN* 1.3 94.8 - - + +
422D GLY* 1.3 67.0 + - - +
423D GLN 3.6 1.6 - - - -
424D ALA* 3.3 9.6 + - - +
425D GLY 3.1 17.7 + - - -
462D ASN* 3.4 55.4 - - + -
465D ARG* 3.8 38.1 - - + +
466D ALA* 3.5 22.2 - - - +
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Residues in contact with GLY 422 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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274D ASP* 5.3 1.8 - - - -
419D ASN* 3.0 22.3 + - - -
421D PHE* 1.3 76.3 - - - +
423D GLN* 1.3 56.4 + - - +
425D GLY* 3.0 17.2 + - - -
426D GLU* 3.1 17.9 + - - +
429D ARG* 4.3 3.6 + - - -
466D ALA 5.0 0.8 - - - +
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Residues in contact with GLN 423 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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175D ASN* 3.4 18.5 + - + +
274D ASP* 5.3 0.2 - - - +
275D PHE* 3.7 30.7 - - + -
282D LYS* 3.6 22.6 - - + +
283D ASP* 3.0 46.9 + - - +
285D PHE* 3.9 23.1 - - + -
419D ASN* 3.8 10.5 + - - +
422D GLY* 1.3 70.5 - - - +
424D ALA* 1.3 60.1 + - - +
425D GLY 3.2 0.2 - - - -
426D GLU* 3.3 24.5 + - - +
427D VAL* 2.8 34.0 + - - +
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Residues in contact with ALA 424 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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174D THR* 3.8 18.2 - - + -
175D ASN* 3.2 43.4 + - + +
178D MET* 3.4 19.4 - - + +
420D ASN 4.3 1.9 + - - +
421D PHE* 3.3 15.0 + - - +
422D GLY 3.2 0.8 - - - -
423D GLN* 1.3 78.9 - - - +
425D GLY* 1.3 56.1 + - - +
427D VAL* 3.5 1.0 + - - +
428D TYR 3.1 20.6 + - - -
466D ALA* 4.1 2.9 - - + -
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Residues in contact with GLY 425 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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421D PHE 3.1 6.3 + - - -
422D GLY 3.0 7.5 + - - -
424D ALA* 1.3 74.3 - - - +
426D GLU* 1.3 63.9 + - - +
428D TYR* 3.1 7.9 + - - +
429D ARG* 2.9 38.7 + - - +
466D ALA* 3.3 29.3 - - - +
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Residues in contact with GLU 426 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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274D ASP* 3.8 20.4 - - - +
285D PHE* 3.9 23.5 - - + -
422D GLY 3.1 12.4 + - - +
423D GLN* 3.3 31.8 + - - +
425D GLY* 1.3 73.2 - - - +
427D VAL* 1.3 61.9 + - - +
429D ARG* 3.2 16.9 + - - +
430D ARG* 3.0 35.3 + - - +
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Residues in contact with VAL 427 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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175D ASN* 3.3 23.1 - - - +
178D MET* 4.0 17.0 - - + -
179D HIS* 3.6 34.8 - - + +
283D ASP* 5.4 1.8 - - + +
285D PHE* 4.0 22.2 - - + -
423D GLN* 2.8 20.2 + - - +
424D ALA 3.6 2.5 - - - +
425D GLY 3.2 0.2 - - - -
426D GLU* 1.3 71.6 - - - +
428D TYR* 1.3 63.7 + - - +
430D ARG* 3.1 20.7 + - - +
431D MET* 3.5 21.8 + - + +
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Residues in contact with TYR 428 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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178D MET* 3.9 12.6 - - + -
424D ALA 3.1 14.7 + - - +
425D GLY* 3.1 7.6 + - - +
427D VAL* 1.3 75.8 - - - +
429D ARG* 1.3 63.4 + - + +
431D MET* 3.3 24.8 - - - +
436D GLN* 3.0 65.5 + - + +
439D LEU* 3.5 32.3 - - + -
467D ASP* 3.6 38.6 - - + -
469D SER* 4.3 4.7 + - - -
470D LEU* 3.6 29.7 - - + +
473D LYS* 3.9 20.1 + - - +
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Residues in contact with ARG 429 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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422D GLY 4.3 4.2 + - - -
425D GLY* 2.9 32.1 + - - +
426D GLU* 3.2 15.6 + - - +
428D TYR* 1.3 79.7 - - + +
430D ARG* 1.3 59.4 + - - +
431D MET 3.2 8.6 + - - +
436D GLN* 4.2 7.4 + - - +
466D ALA 3.2 20.8 + - - -
467D ASP* 2.9 42.7 + - - +
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Residues in contact with ARG 430 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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285D PHE* 3.4 54.4 - - - +
286D GLU 5.5 0.2 - - - +
287D ASP* 2.9 42.6 + - - -
288D VAL* 4.6 3.0 - - - +
426D GLU* 3.0 24.8 + - - +
427D VAL* 3.1 10.0 + - - +
429D ARG* 1.3 74.7 - - - +
431D MET* 1.3 64.7 + - - +
432D THR* 5.4 1.4 - - - +
435D GLU* 4.6 1.2 - - - +
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Residues in contact with MET 431 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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178D MET* 3.4 28.5 - - + +
179D HIS* 5.4 0.4 - - + -
182D THR* 3.8 18.6 - - + -
427D VAL* 3.6 20.6 - - + +
428D TYR* 3.3 42.0 - - - +
429D ARG 3.2 7.9 - - - +
430D ARG* 1.3 82.2 - - - +
432D THR* 1.3 70.9 + - - +
435D GLU* 3.3 32.5 - - + +
436D GLN* 3.7 8.8 + - + -
439D LEU* 4.2 10.3 - - + -
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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