Contacts of the helix formed by residues 25 - 35 (chain X) 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 25 (chain X).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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23X ARG 3.7 2.9 - - - +
24X LEU* 1.3 93.4 - - + +
26X GLY* 1.3 65.0 + - - +
27X HIS* 3.5 29.2 - - + +
28X TYR* 3.4 9.3 + - + -
29X LEU* 3.4 20.7 + - - +
203X TRP* 3.5 45.3 - - + +
215X GLN* 5.9 0.2 - - - +
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Residues in contact with GLY 26 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24X LEU 3.9 0.4 + - - -
25X PRO* 1.3 74.2 - - - +
27X HIS* 1.3 62.9 + - - +
28X TYR 3.4 0.3 + - - -
29X LEU* 3.6 6.4 + - - +
30X ARG* 3.0 45.3 + - - +
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Residues in contact with HIS 27 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25X PRO* 3.5 21.6 - - + +
26X GLY* 1.3 75.3 + - - +
28X TYR* 1.3 79.7 + - + +
30X ARG* 3.7 25.7 - - - +
31X SER* 4.0 5.4 + - - -
199X GLU* 4.9 7.9 - - + -
200X GLU* 3.8 52.7 + - + +
203X TRP* 3.6 25.8 - + + -
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Residues in contact with TYR 28 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24X LEU* 3.9 27.6 - - + -
25X PRO* 3.4 19.8 + - + +
26X GLY 3.3 0.6 - - - -
27X HIS* 1.3 80.3 - - + +
29X LEU* 1.3 62.4 + - - +
30X ARG 3.1 1.8 - - - -
31X SER* 2.6 48.0 + - - -
32X LEU* 3.5 31.0 + - + +
203X TRP* 4.2 38.4 - + + -
204X VAL* 6.1 0.2 - - - -
205X GLY 6.2 0.2 - - - -
206X LEU* 3.9 11.7 + - + -
207X THR 2.8 29.2 + - - -
208X LEU* 3.6 2.7 + - + -
211X ALA* 3.2 27.7 - - + +
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Residues in contact with LEU 29 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16X LEU* 4.5 25.1 - - + +
21X CYS 3.5 27.1 - - - +
22X SER* 4.7 5.8 - - - +
24X LEU* 4.1 24.7 - - + +
25X PRO 3.4 13.0 + - - +
26X GLY* 3.6 6.7 + - - +
28X TYR* 1.3 76.6 - - + +
30X ARG* 1.3 55.6 + - - +
32X LEU* 3.2 27.2 + - + +
33X GLU* 2.9 47.0 + - - +
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Residues in contact with ARG 30 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26X GLY* 3.0 34.3 + - - +
27X HIS* 3.7 16.3 - - - +
28X TYR 3.1 0.4 - - - -
29X LEU* 1.3 76.9 - - - +
31X SER* 1.3 55.8 + - - +
33X GLU* 3.2 14.0 + - - +
34X GLU* 2.9 39.6 + - + +
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Residues in contact with SER 31 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27X HIS 4.0 5.2 + - - -
28X TYR* 2.6 37.8 + - - -
30X ARG* 1.3 77.0 - - - +
32X LEU* 1.3 69.9 + - - +
34X GLU* 3.3 34.3 + - - +
35X GLU 4.2 2.3 + - - -
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Residues in contact with LEU 32 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16X LEU* 5.2 9.4 - - + -
28X TYR* 3.5 47.1 + - + +
29X LEU* 3.2 30.7 + - + +
31X SER* 1.3 83.7 + - - +
33X GLU* 1.3 62.8 + - + +
34X GLU 3.5 0.2 + - - -
35X GLU* 4.2 17.2 + - - +
206X LEU 5.4 2.9 - - - +
208X LEU* 4.2 30.3 - - + +
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Residues in contact with GLU 33 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13X ARG* 6.3 3.1 - - - -
16X LEU* 5.1 13.6 - - + +
29X LEU* 2.9 37.9 + - - +
30X ARG* 3.5 12.5 + - - +
32X LEU* 1.3 77.9 - - + +
34X GLU* 1.3 66.2 + - - +
35X GLU* 4.3 3.4 - - - +
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Residues in contact with GLU 34 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30X ARG* 2.9 17.8 + - + +
31X SER* 3.3 29.3 + - - +
33X GLU* 1.3 79.1 - - - +
35X GLU* 1.3 71.9 + - - +
36X ARG* 2.7 41.3 + - + +
151X GLU* 4.8 0.2 - - - +
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Residues in contact with GLU 35 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31X SER 4.2 3.8 + - - -
32X LEU 4.2 13.1 + - - +
33X GLU 4.3 4.7 - - - +
34X GLU* 1.3 82.7 - - - +
36X ARG* 1.3 65.9 + - - +
151X GLU* 2.8 20.8 + - - +
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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