Contacts of the helix formed by residues 25 - 32 (chain B) in PDB entry 5X1V
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 THR 25 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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397A GLU* 3.5 28.3 - - + -
400A ARG* 5.4 7.6 - - + -
401A LEU* 3.9 26.3 - - + +
23B ALA* 4.0 0.9 - - - +
24B ASP* 1.3 88.1 - - + +
26B PHE* 1.3 59.4 + - - +
27B LEU* 3.8 1.0 + - - +
28B GLU* 3.0 27.8 + - - +
29B HIS* 3.0 25.3 + - - +
390B TYR* 3.2 12.8 + - - -
24C ASP* 5.8 2.7 - - - +
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Residues in contact with PHE 26 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26A PHE* 4.1 37.9 - + - -
393A GLN* 3.5 23.3 - - + +
397A GLU* 3.0 11.8 + - - +
25B THR* 1.3 67.3 - - - +
27B LEU* 1.3 60.4 + - - +
29B HIS* 3.4 7.5 - + - +
30B MET* 3.0 53.8 + - + +
390B TYR* 3.6 35.9 - + + -
393B GLN* 3.8 10.8 - - - +
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Residues in contact with LEU 27 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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315A GLY* 3.6 33.4 - - - +
318A ASN* 4.4 10.3 - - + +
319A ARG* 5.0 5.6 - - + -
394A LEU* 4.8 11.4 - - + -
397A GLU* 2.8 31.4 + - + +
398A LEU* 3.8 36.1 - - + +
401A LEU* 4.5 16.8 - - + -
25B THR* 4.1 3.4 - - - +
26B PHE* 1.3 75.4 - - - +
28B GLU* 1.3 55.6 + - - +
30B MET* 3.1 16.2 + - + +
31B CYS* 2.9 32.4 + - - -
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Residues in contact with GLU 28 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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319A ARG* 2.6 37.8 + - - -
401A LEU* 4.5 10.7 - - + +
19B HIS* 5.4 0.2 + - - -
23B ALA* 3.8 11.9 - - + -
24B ASP 5.1 1.3 - - - +
25B THR* 3.0 21.8 + - - +
27B LEU* 1.3 73.3 - - - +
29B HIS* 1.3 59.6 + - - +
31B CYS* 3.3 4.6 + - - +
32B ARG* 2.9 70.4 + - - +
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Residues in contact with HIS 29 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17B GLN 5.3 0.2 - - - -
20B ALA* 2.7 46.3 + - + +
21B ALA* 4.3 2.9 - - - -
23B ALA* 3.5 7.2 - - - +
25B THR 3.0 14.7 + - - +
26B PHE* 3.4 15.3 - + - +
28B GLU* 1.3 75.4 - - - +
30B MET* 1.3 67.9 + - + +
32B ARG 3.4 7.8 + - - -
33B LEU* 3.4 23.3 + - + +
387B ALA 5.1 1.8 - - - -
388B ALA* 2.6 32.0 + - - -
389B ILE 3.7 14.1 - - - -
390B TYR* 3.5 39.2 + + + -
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Residues in contact with MET 30 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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311A LYS* 3.5 43.5 - - + +
312A MET* 3.3 14.9 + - - -
314A ILE* 4.7 0.2 - - + -
315A GLY* 4.3 12.8 - - - +
354A ASP* 3.5 39.7 - - + +
26B PHE* 3.0 45.1 + - + +
27B LEU* 3.4 16.8 - - + +
29B HIS* 1.3 78.1 - - + +
31B CYS* 1.3 62.4 + - - +
33B LEU* 3.2 26.1 + - + +
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Residues in contact with CYS 31 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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311A LYS 4.4 0.2 + - - -
312A MET* 3.4 8.9 - - - +
315A GLY 3.5 30.1 - - - -
316A ARG* 2.9 45.3 + - + +
319A ARG* 3.5 37.2 - - - +
27B LEU* 2.9 25.3 + - - -
28B GLU* 3.5 11.9 - - - +
30B MET* 1.3 74.4 - - - +
32B ARG* 1.3 56.7 + - - +
33B LEU 3.4 0.2 - - - -
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Residues in contact with ARG 32 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
316A ARG* 4.7 4.9 - - - +
17B GLN* 4.2 0.7 - - - +
19B HIS* 2.8 78.4 + - + +
20B ALA* 3.7 25.3 + - + +
22B MET* 3.6 8.7 + - - +
23B ALA* 3.3 27.7 - - - +
28B GLU* 2.9 46.9 + - - +
29B HIS 3.9 0.4 - - - -
30B MET 3.2 0.6 + - - -
31B CYS* 1.3 76.3 - - - +
33B LEU* 1.4 63.9 + - - +
34B ASP* 3.3 12.0 + - - +
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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