Contacts of the helix formed by residues 30 - 38 (chain X) in PDB entry 2JFE
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 CYS 30 (chain X).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16X TYR* 4.3 12.6 - - - -
27X LYS* 4.6 3.4 - - - -
28X GLY 3.5 0.8 + - - -
29X PRO* 1.3 75.5 - - - +
31X VAL* 1.3 64.3 + - - +
32X TRP* 3.6 19.5 - - - -
33X ASP* 2.7 39.0 + - - +
34X THR* 3.4 9.5 + - - -
79X SER* 5.8 0.4 - - - +
81X SER* 3.5 19.3 - - - +
122X ASP* 3.7 23.6 - - + +
123X LEU 3.4 14.4 - - - +
124X PRO* 4.1 0.4 - - - -
125X GLN* 3.8 4.5 - - - +
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Residues in contact with VAL 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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30X CYS* 1.3 71.5 - - - +
32X TRP* 1.3 72.1 + - + +
34X THR* 3.4 3.2 + - - -
35X PHE* 2.8 28.9 + - - +
121X PHE 4.3 3.4 - - - +
122X ASP 4.4 0.2 - - - -
123X LEU* 2.9 40.1 + - + +
125X GLN* 3.6 16.8 - - - +
128X GLU* 3.6 39.7 - - + +
180X PRO* 3.6 30.4 - - + +
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Residues in contact with TRP 32 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16X TYR* 3.3 28.7 - + + -
30X CYS* 3.3 2.8 - - - -
31X VAL* 1.3 82.8 - - + +
33X ASP* 1.3 65.3 + - - +
35X PHE* 3.6 26.0 - + - -
36X THR* 2.8 50.9 + - + +
43X VAL* 4.7 2.5 - - + -
121X PHE* 2.8 31.4 + - - +
122X ASP* 4.5 5.8 - - + -
179X PHE* 3.6 41.3 - + - +
180X PRO* 3.7 16.3 - - + +
423X PHE* 4.1 7.0 - + - -
425X TRP* 3.3 61.7 - + + -
426X ASN* 4.4 4.3 - - - -
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Residues in contact with ASP 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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16X TYR* 3.6 15.9 + - - -
22X TRP* 3.1 47.6 - - + +
27X LYS* 3.0 17.7 + - - -
29X PRO* 3.6 7.8 - - + +
30X CYS* 2.7 36.8 + - - +
32X TRP* 1.3 79.6 - - - +
34X THR* 1.3 60.8 + - - +
36X THR* 4.4 0.9 - - - -
37X HIS* 3.0 34.2 + - - -
50X ASP* 5.0 0.5 - - - +
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Residues in contact with THR 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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29X PRO* 4.7 5.5 - - - +
30X CYS 3.4 3.7 + - - -
31X VAL 3.4 3.2 + - - -
32X TRP 3.3 0.4 - - - -
33X ASP* 1.3 76.6 - - - +
35X PHE* 1.3 64.5 + - - +
37X HIS* 3.6 5.1 + - - +
38X GLN* 3.3 38.1 + - + +
125X GLN* 2.6 42.8 + - + +
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Residues in contact with PHE 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 VAL 2.8 22.5 + - - +
32X TRP* 3.6 33.9 - + - +
34X THR* 1.3 72.7 - - - +
36X THR* 1.3 62.4 + - - +
38X GLN* 3.1 27.0 + - - +
39X GLY 4.0 4.5 + - - +
42X ARG* 3.2 69.2 + - + +
43X VAL* 4.3 7.9 - - + -
177X GLY 5.4 0.2 - - - -
178X MET 3.3 25.8 - - - -
179X PHE 4.2 2.5 - - - -
180X PRO* 3.6 33.2 - - + -
181X PRO 5.2 1.3 - - - -
182X GLY* 4.4 2.2 - - - -
426X ASN* 4.0 5.2 - - - -
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Residues in contact with THR 36 (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 TYR* 3.4 14.5 + - - +
32X TRP* 2.8 49.3 + - + +
35X PHE* 1.3 72.1 - - - +
37X HIS* 1.3 69.3 + - - +
38X GLN 3.3 0.7 + - - -
39X GLY* 3.6 9.6 + - - +
43X VAL* 4.0 15.0 - - + -
46X ASN* 4.6 7.8 - - - +
47X GLN 3.8 13.6 - - - +
48X THR* 3.4 25.5 - - - +
423X PHE* 3.9 17.3 - - + -
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Residues in contact with HIS 37 (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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22X TRP* 3.5 47.9 - + - -
33X ASP* 3.0 25.6 + - - +
34X THR* 4.1 5.1 - - - +
35X PHE 3.3 0.4 - - - -
36X THR* 1.3 88.3 + - - +
38X GLN* 1.3 60.5 + - - +
39X GLY 3.4 0.7 + - - -
48X THR* 4.2 8.3 - - + -
50X ASP* 2.9 28.7 + - - -
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Residues in contact with GLN 38 (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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1A NAG 3.7 6.7 + - - -
34X THR* 3.3 32.7 + - + +
35X PHE* 3.1 16.9 + - - +
37X HIS* 1.3 76.4 - - - +
39X GLY* 1.3 65.2 + - - +
40X GLY 3.5 1.6 + - - -
42X ARG* 3.1 28.6 - - - +
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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