Contacts of the helix formed by residues 25 - 34 (chain P) in PDB entry 2I2X
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 P).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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416O ARG* 6.2 4.0 - - - +
23P ALA 4.7 4.3 - - - +
24P LEU* 1.3 77.0 - - - +
26P PRO* 1.4 75.9 - - - +
27P GLU* 3.6 13.3 + - - +
28P GLU* 2.7 43.9 + - - +
29P ALA* 3.0 21.4 + - - +
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Residues in contact with PRO 26 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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417O PHE* 4.3 18.4 - - + -
24P LEU 4.0 1.5 - - - +
25P THR* 1.4 87.4 - - + +
27P GLU* 1.3 69.5 + - - +
29P ALA* 3.3 3.5 + - + +
30P ALA* 2.9 30.5 + - - +
48P PHE* 3.7 18.4 - - + -
87P LEU* 4.1 1.7 - - - +
92P VAL* 4.0 28.0 - - + +
93P ILE* 4.1 13.5 - - + -
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Residues in contact with GLU 27 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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420O LYS* 5.2 9.9 + - - -
25P THR* 3.6 15.1 + - - +
26P PRO* 1.3 94.5 - - - +
28P GLU* 1.3 59.3 + - + +
30P ALA* 3.3 3.2 + - - +
31P GLU* 2.9 30.2 + - - +
34P TYR* 5.0 1.6 - - - -
48P PHE* 4.3 19.7 - - + -
49P GLU* 5.9 3.8 - - + +
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Residues in contact with GLU 28 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23P ALA 4.5 1.4 - - - +
24P LEU* 3.6 22.3 - - + +
25P THR* 2.7 50.1 + - - +
27P GLU* 1.3 79.9 - - + +
29P ALA* 1.3 61.4 + - - +
31P GLU* 3.2 9.2 + - - +
32P GLU* 3.2 26.7 + - - +
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Residues in contact with ALA 29 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24P LEU* 3.9 24.2 - - + +
25P THR 3.0 15.8 + - - +
26P PRO 3.5 5.8 - - - +
28P GLU* 1.3 75.8 - - - +
30P ALA* 1.3 61.6 + - - +
32P GLU* 3.6 11.4 + - - +
33P LEU* 3.4 22.0 + - - +
87P LEU* 3.9 21.3 - - + +
90P GLU* 5.8 0.4 - - - +
92P VAL* 4.3 11.7 - - + -
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Residues in contact with ALA 30 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26P PRO 2.9 16.4 + - - +
27P GLU 3.6 4.7 - - - +
29P ALA* 1.3 75.3 - - - +
31P GLU* 1.3 58.1 + - - +
33P LEU* 3.0 17.2 + - - +
34P TYR* 3.0 43.2 + - + +
48P PHE* 3.8 25.6 - - + -
83P VAL* 4.4 6.3 - - + -
87P LEU* 3.8 10.2 - - + +
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Residues in contact with GLU 31 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27P GLU 2.9 14.2 + - - +
28P GLU* 3.2 13.9 + - - +
30P ALA* 1.3 73.6 - - - +
32P GLU* 1.3 64.5 + - - +
33P LEU 3.4 0.3 + - - -
34P TYR* 3.4 24.7 + - - +
41P TYR* 2.7 40.3 + - - -
45P LYS* 5.0 5.4 + - - +
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Residues in contact with GLU 32 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24P LEU* 3.5 34.2 - - - +
28P GLU 3.2 12.0 + - - +
29P ALA* 3.8 9.2 - - - +
30P ALA 3.3 0.4 - - - -
31P GLU* 1.3 76.4 - - - +
33P LEU* 1.3 67.9 + - + +
34P TYR 3.7 3.6 + - - +
36P LYS* 4.7 9.0 + - - +
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Residues in contact with LEU 33 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29P ALA 3.4 9.9 - - - +
30P ALA 3.0 9.4 + - - +
32P GLU* 1.3 85.3 - - + +
34P TYR* 1.3 63.8 + - - +
35P PRO* 3.5 2.8 - - - +
36P LYS* 5.4 1.9 + - - -
79P VAL* 5.9 0.3 - - - +
83P VAL* 3.7 34.6 - - + +
86P ARG* 3.2 59.2 - - + +
87P LEU* 3.8 22.4 - - + -
90P GLU* 5.1 1.3 - - - +
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Residues in contact with TYR 34 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27P GLU* 5.0 1.7 + - - -
30P ALA* 3.0 30.0 + - + +
31P GLU* 3.4 34.1 - - - +
32P GLU 3.4 2.6 - - - +
33P LEU* 1.3 80.3 - - - +
35P PRO* 1.4 65.4 - - + +
36P LYS* 3.1 26.6 + - + +
41P TYR* 3.6 35.0 - + + -
44P ALA* 3.8 21.8 - - + -
45P LYS* 3.4 42.2 - - + +
48P PHE* 3.3 36.0 - - + +
49P GLU* 5.2 0.3 + - - -
83P VAL* 4.8 10.3 - - + -
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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