Contacts of the helix formed by residues 362 - 369 (chain 6) in PDB entry 3J7Y
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 362 (chain 6).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1463 GLU* 4.0 14.1 - - + +
1473 PHE 3.3 17.9 - - - +
1483 VAL* 5.1 0.4 - - - -
1493 PHE* 3.9 4.3 - - - -
3606 ARG 4.5 2.0 - - - +
3616 GLN* 1.3 93.5 - - + +
3636 LEU* 1.3 60.4 + - - +
3646 ARG* 3.0 53.6 - - + +
3656 TYR* 3.0 24.4 + - - +
3686 ARG* 5.0 8.5 - - - +
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Residues in contact with LEU 363 (chain 6).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1173 LEU* 4.5 1.8 - - + -
1233 VAL* 4.3 11.0 - - + -
1473 PHE* 4.0 30.4 + - + +
1483 VAL* 5.2 0.6 - - - +
1493 PHE* 3.7 30.5 - - + -
1773 TYR* 3.5 37.7 - - + -
1803 TYR* 3.5 54.7 - - + +
3626 PRO* 1.3 74.3 - - - +
3646 ARG* 1.3 60.0 + - + +
3656 TYR 3.1 1.9 + - - -
3666 LEU* 3.7 5.5 + - - +
3676 ASP* 4.5 0.9 - - - -
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Residues in contact with ARG 364 (chain 6).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1423 LYS* 3.6 6.1 - - - +
1463 GLU* 2.7 39.1 + - - +
3626 PRO* 3.7 21.0 - - + +
3636 LEU* 1.3 75.7 - - - +
3656 TYR* 1.3 65.5 + - - +
3666 LEU 3.2 1.3 - - - -
3676 ASP* 3.1 26.5 + - + +
3686 ARG* 3.5 16.8 + - - +
2858A A 3.0 56.7 + - - -
2859A A 2.7 36.7 + - - +
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Residues in contact with TYR 365 (chain 6).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1493 PHE* 3.9 13.2 - - + -
3526 PRO* 4.6 7.3 - - + +
3536 LYS 3.0 25.8 + - - -
3546 GLN* 3.5 22.2 - - - -
3556 LYS* 3.3 20.3 + - + +
3586 PRO* 3.9 21.8 - - + -
3616 GLN* 3.6 35.9 - - + -
3626 PRO* 3.0 18.2 + - - +
3636 LEU 3.1 0.4 - - - -
3646 ARG* 1.3 79.7 - - - +
3666 LEU* 1.3 66.8 + - + +
3686 ARG* 3.4 24.1 + - - +
3696 TYR* 3.2 49.4 + + - -
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Residues in contact with LEU 366 (chain 6).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1173 LEU* 4.1 3.6 - - + -
1193 CYS* 5.3 1.1 - - - -
1213 LEU* 4.3 7.4 - - + -
1493 PHE* 3.7 23.8 - - + -
1803 TYR* 3.6 55.0 - - + +
1823 ASP 5.2 2.2 - - - +
1833 ARG* 4.0 39.7 - - + +
1843 THR* 4.5 1.4 + - - +
3546 GLN* 4.9 4.5 - - - +
3586 PRO* 5.4 0.2 - - + -
3636 LEU 3.7 0.8 + - - -
3646 ARG 3.2 1.0 - - - -
3656 TYR* 1.3 85.1 - - + +
3676 ASP* 1.3 61.6 + - - +
3686 ARG 3.5 0.2 + - - -
3696 TYR* 3.2 23.3 + - - +
3706 ARG* 3.1 16.4 + - - +
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Residues in contact with ASP 367 (chain 6).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1793 LYS* 2.7 27.3 + - - -
1803 TYR* 2.8 25.7 + - - -
3646 ARG* 3.1 24.1 + - + +
3666 LEU* 1.3 73.4 - - - +
3686 ARG* 1.3 62.3 + - + +
3696 TYR 3.3 0.6 + - - -
3706 ARG* 2.9 32.3 + - - +
2859A A 6.1 1.1 - - - +
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Residues in contact with ARG 368 (chain 6).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3516 HIS* 3.6 30.6 + - + +
3616 GLN* 4.4 17.6 - - - +
3626 PRO* 5.0 6.5 - - - +
3646 ARG* 3.6 18.8 - - - +
3656 TYR* 3.5 37.1 + - - +
3666 LEU 3.3 0.6 - - - -
3676 ASP* 1.3 78.5 - - - +
3696 TYR* 1.3 75.5 + - + +
3706 ARG 3.8 2.1 + - - -
2859A A 2.9 54.8 + - - +
2860A G 3.0 37.2 + - - -
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Residues in contact with TYR 369 (chain 6).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1843 THR* 2.7 30.7 + - - +
1853 ASN* 5.1 11.2 - - + +
3516 HIS* 3.6 19.1 - + + +
3526 PRO* 3.2 46.3 + - - +
3546 GLN* 3.5 33.8 - - + +
3656 TYR* 3.2 62.6 + + - -
3666 LEU* 3.2 9.3 + - - +
3686 ARG* 1.3 89.1 + - + +
3706 ARG* 1.3 54.3 + - - +
2860A G 4.1 2.6 + - - -
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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