Contacts of the helix formed by residues 22 - 28 (chain Q) in PDB entry 2D2C
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 LEU 22 (chain Q).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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271P MET* 3.3 38.0 - - + +
274P LEU* 5.3 1.8 - - + -
19Q MET* 2.9 38.7 + - + +
20Q ASN* 3.8 2.2 - - - +
21Q LEU* 1.3 79.0 - - - +
23Q ALA* 1.3 73.6 + - + +
24Q PHE 3.2 1.3 - - - -
25Q GLY* 3.4 3.8 - - - +
26Q THR* 2.6 44.6 + - + +
21U VAL* 6.3 2.9 - - + -
24U ARG* 6.2 1.8 - - - +
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Residues in contact with ALA 23 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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268P ALA 4.3 0.2 - - - +
271P MET* 2.9 41.5 - - + +
272P LEU* 4.3 1.8 + - - -
275P LYS* 4.7 4.7 - - + -
19Q MET* 5.0 1.8 - - + -
20Q ASN* 3.0 33.7 - - + +
22Q LEU* 1.3 86.6 - - + +
24Q PHE* 1.3 63.9 + - + +
26Q THR* 3.1 4.7 + - - -
27Q VAL* 2.8 22.3 - - - +
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Residues in contact with PHE 24 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38O TYR* 3.4 31.9 - + + -
41O PRO* 5.0 2.7 - - + -
1306O OPC 4.8 19.1 - - + -
272P LEU* 3.0 38.4 - - + -
275P LYS* 4.8 17.9 - - + -
20Q ASN* 3.0 21.8 + - - +
21Q LEU* 5.7 0.4 - - - -
23Q ALA* 1.3 77.3 - - + +
25Q GLY* 1.3 57.1 + - - +
26Q THR 2.9 5.4 - - - -
27Q VAL* 3.5 22.2 - - + -
28Q THR* 2.6 45.4 + - + +
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Residues in contact with GLY 25 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21Q LEU* 2.7 29.6 + - - +
22Q LEU* 3.3 1.5 + - - -
24Q PHE* 1.3 78.8 - - - +
26Q THR* 1.3 61.1 + - - +
28Q THR* 3.9 15.6 + - - +
29Q GLY* 4.2 2.9 + - - -
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Residues in contact with THR 26 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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264P LEU* 5.0 4.1 - - - +
267P LEU* 5.0 8.1 - - + -
268P ALA* 3.5 19.9 - - - -
271P MET* 3.2 25.2 - - + +
22Q LEU* 2.6 33.7 + - + +
23Q ALA 3.1 7.4 + - - -
25Q GLY* 1.3 78.9 - - - +
27Q VAL* 1.3 63.1 + - - +
28Q THR 3.3 0.2 - - - -
29Q GLY* 2.6 25.6 + - - -
30Q VAL* 2.8 15.8 + - - +
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Residues in contact with VAL 27 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41O PRO* 5.2 4.3 - - + -
45O MET* 4.4 10.5 - - - -
268P ALA* 3.8 21.8 - - + +
272P LEU* 3.6 35.7 - - + -
23Q ALA 2.8 24.9 - - - +
24Q PHE* 3.5 22.4 - - + +
26Q THR* 1.3 77.1 + - - +
28Q THR* 1.3 58.0 + - + +
29Q GLY 2.4 17.8 + - - -
30Q VAL* 2.6 17.3 + - - +
31Q ALA* 3.3 7.4 + - - +
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Residues in contact with THR 28 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24Q PHE* 2.6 37.7 + - + +
25Q GLY* 3.9 11.8 + - - +
26Q THR 3.6 0.9 - - - -
27Q VAL* 1.3 71.3 - - + +
29Q GLY* 1.3 55.1 + - - +
31Q ALA* 4.4 15.0 - - - -
32Q LEU* 3.9 18.5 - - - +
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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