Contacts of the helix formed by residues 21 - 27 (chain Q) in PDB entry 3A68
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 VAL 21 (chain Q).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135N LEU* 4.7 11.7 - - + -
138N SER* 3.5 41.1 - - - +
139N LEU* 3.7 22.9 - - + +
142N LEU* 4.6 7.2 - - + -
17Q PRO 2.7 24.4 + - - +
18Q PHE* 3.7 24.9 - - + +
20Q GLU* 1.3 73.3 - - - +
22Q LYS* 1.3 69.5 + - - +
23Q LYS 3.4 0.4 - - - -
24Q GLU* 3.6 6.1 - - + -
25Q LEU* 2.9 23.9 + - + +
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Residues in contact with LYS 22 (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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18Q PHE* 3.2 23.7 + - - +
19Q GLU* 3.4 27.6 + - - +
20Q GLU 3.3 0.6 - - - -
21Q VAL* 1.3 85.3 - - - +
23Q LYS* 1.3 65.8 - - + +
25Q LEU* 3.3 12.2 + - - +
26Q ASP* 3.7 16.3 + - - +
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Residues in contact with LYS 23 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19Q GLU 5.5 1.8 - - - +
20Q GLU* 4.2 9.9 + - - +
21Q VAL 3.4 0.4 - - - -
22Q LYS* 1.3 80.5 - - + +
24Q GLU* 1.3 60.7 + - - +
25Q LEU 3.5 0.2 - - - -
26Q ASP* 3.9 7.1 + - - +
27Q LEU* 3.3 27.1 + - + +
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Residues in contact with GLU 24 (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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138N SER* 3.4 32.8 + - - +
141N LYS* 3.9 27.2 + - + +
142N LEU* 4.6 8.9 + - + +
145N GLU* 4.3 13.7 - - - +
20Q GLU 4.3 5.5 + - - +
21Q VAL* 3.1 19.8 + - + +
23Q LYS* 1.3 78.1 - - - +
25Q LEU* 1.3 62.3 + - - +
26Q ASP 3.2 1.8 - - - -
27Q LEU* 3.3 41.2 + - - +
28Q VAL* 3.7 5.7 + - - +
39Q GLN* 5.1 4.6 + - - -
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Residues in contact with LEU 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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126N LYS* 6.1 2.9 - - - -
131N HIS* 4.4 14.6 - - + +
134N GLU* 3.7 40.1 - - + +
135N LEU* 3.5 28.7 - - + +
138N SER* 3.1 22.2 + - - +
21Q VAL* 2.9 16.6 + - + +
22Q LYS* 3.3 6.9 + - - +
24Q GLU* 1.3 76.9 - - - +
26Q ASP* 1.3 65.8 + - - +
28Q VAL* 3.1 19.8 - - + +
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Residues in contact with ASP 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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22Q LYS 3.7 12.5 + - - +
23Q LYS* 3.9 9.4 + - - +
24Q GLU 3.2 0.6 - - - -
25Q LEU* 1.3 82.8 - - - +
27Q LEU* 1.3 61.2 + - - +
28Q VAL 3.1 13.2 + - - +
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Residues in contact with LEU 27 (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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141N LYS* 5.7 3.0 + - - +
23Q LYS* 3.3 18.8 + - + +
24Q GLU* 3.3 37.1 + - - +
26Q ASP* 1.3 75.6 - - - +
28Q VAL* 1.3 63.7 + - - +
29Q PRO* 3.1 11.5 - - - +
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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