Contacts of the helix formed by residues 26 - 33 (chain D) in PDB entry 2P1N
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 SER 26 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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22D VAL 4.6 0.2 + - - -
23D ALA 3.3 6.0 + - - +
24D LEU 3.2 9.4 - - - +
25D GLU* 1.3 76.2 - - - +
27D GLN* 1.3 60.8 + - - +
29D ILE* 2.8 36.8 + - - +
30D ALA* 3.2 14.7 + - - +
59D CYS* 5.2 0.4 - - - -
108D LEU* 2.4 44.8 + - - +
109D ASN 3.8 2.0 - - - -
110D ILE* 3.7 11.0 - - - +
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Residues in contact with GLN 27 (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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24D LEU 5.3 3.1 - - - +
25D GLU 3.6 3.2 + - - -
26D SER* 1.3 71.0 - - - +
28D THR* 1.3 67.5 + - - +
30D ALA* 3.3 15.1 + - + +
31D HIS* 2.9 42.4 - - + +
109D ASN* 3.1 39.8 + - + +
111D LYS* 5.5 2.9 + - - +
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Residues in contact with THR 28 (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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26D SER* 3.5 1.8 - - - -
27D GLN* 1.3 78.3 - - - +
29D ILE* 1.3 63.8 + - - +
31D HIS* 3.3 4.4 + - - +
32D MET* 3.1 44.9 + - + +
44D LEU* 5.6 0.4 - - + -
107D TYR* 2.5 39.4 + - + +
108D LEU* 3.0 25.0 + - + -
109D ASN* 3.8 13.1 + - - +
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Residues in contact with ILE 29 (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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6D ILE* 5.1 2.2 - - + -
8D LEU* 4.3 17.9 - - + -
23D ALA* 3.5 34.3 - - + +
24D LEU* 5.3 1.3 - - + -
26D SER* 2.8 28.1 + - - +
28D THR* 1.3 72.7 - - - +
30D ALA* 1.3 55.1 + - - +
31D HIS 2.7 2.1 + - - -
32D MET* 2.7 28.7 + - - +
33D VAL* 3.0 23.8 + - + -
42D VAL* 4.2 15.3 - - + -
44D LEU* 3.5 37.7 - - + -
108D LEU* 3.8 12.3 - - + -
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Residues in contact with ALA 30 (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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24D LEU* 3.3 35.2 - - + +
26D SER 3.2 11.1 + - - +
27D GLN* 3.3 17.9 + - + +
29D ILE* 1.3 77.6 - - - +
31D HIS* 1.3 64.5 + - + +
33D VAL* 3.4 23.1 - - - +
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Residues in contact with HIS 31 (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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27D GLN* 2.9 42.5 + - + +
28D THR* 3.9 4.3 - - - +
29D ILE 2.7 2.0 + - - -
30D ALA* 1.3 80.6 + - + +
32D MET* 1.3 66.0 + - - +
33D VAL 3.4 6.0 - - - -
109D ASN* 5.8 2.0 - - - -
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Residues in contact with MET 32 (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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28D THR* 3.1 34.1 + - + +
29D ILE* 2.7 12.9 + - - +
31D HIS* 1.3 75.3 - - - +
33D VAL* 1.3 61.8 + - - +
42D VAL* 4.4 19.5 - - + +
43D PRO* 4.4 12.1 - - + +
44D LEU* 4.4 17.3 - - - -
45D PRO* 5.4 2.9 - - + -
107D TYR* 4.0 22.4 - - + +
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Residues in contact with VAL 33 (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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6D ILE* 5.5 14.6 - - + -
24D LEU* 5.2 6.7 - - + -
29D ILE* 3.0 26.2 + - + +
30D ALA* 3.4 21.8 - - - +
31D HIS 3.9 7.0 - - - -
32D MET* 1.3 77.6 - - - +
42D VAL* 5.0 10.4 - - + +
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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