Contacts of the helix formed by residues 35 - 45 (chain Q) in PDB entry 1P7G
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 35 (chain Q).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31Q GLU* 3.7 14.6 - - - -
32Q PRO 5.2 0.4 - - - -
34Q ILE* 1.3 75.3 - - - +
36Q ALA* 1.3 58.6 + - - +
37Q GLU* 3.3 13.0 + - - +
38Q ILE* 3.1 28.4 + - - +
39Q MSE 3.0 31.3 + - - +
184Q LEU* 5.4 0.2 - - - +
185Q GLN* 2.5 26.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 36 (chain Q).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27Q TYR* 3.1 28.2 - - + +
28Q ASN* 3.7 22.4 - - + +
31Q GLU* 3.5 14.2 + - - +
35Q SER* 1.3 73.6 - - - +
37Q GLU* 1.3 57.8 + - - +
39Q MSE 3.4 1.6 + - - +
40Q GLN* 3.0 31.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 37 (chain Q).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35Q SER* 3.2 9.2 + - - +
36Q ALA* 1.3 76.2 - - - +
38Q ILE* 1.3 60.5 + - - +
40Q GLN* 3.3 6.2 + - - +
41Q LEU* 2.9 37.1 + - + +
184Q LEU* 3.5 34.9 - - + +
187S LYS* 3.7 22.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 38 (chain Q).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34Q ILE* 3.8 13.9 - - + -
35Q SER* 3.1 16.7 + - - +
37Q GLU* 1.3 78.1 - - - +
39Q MSE 1.3 65.1 + - - +
41Q LEU* 4.0 2.0 - - - +
42Q HIS* 2.8 34.0 + - + +
180Q HIS 3.9 16.1 - - - +
181Q ALA* 3.7 20.4 - - - +
182Q TYR* 3.7 22.4 - - - +
184Q LEU* 4.0 23.3 - - + +
185Q GLN* 3.6 39.0 - - + +
186Q TYR* 5.3 0.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MSE 39 (chain Q).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23Q LEU* 4.5 7.5 - - + +
25Q TYR* 3.7 20.9 - - + +
27Q TYR* 3.3 34.7 - - + +
30Q LEU* 3.6 31.6 - - + -
34Q ILE* 3.6 32.1 - - + +
35Q SER 3.0 21.4 + - - +
36Q ALA 3.7 0.7 - - - +
38Q ILE* 1.3 78.1 - - - +
40Q GLN* 1.3 56.6 + - - +
42Q HIS* 3.8 4.4 - - - +
43Q HIS* 3.1 29.8 + - - +
93Q PHE* 5.8 0.9 - - - -
94Q TRP* 3.6 35.8 - - + -
97Q MSE 4.2 1.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 40 (chain Q).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27Q TYR* 3.3 32.8 - - + +
36Q ALA 3.0 19.2 + - - +
37Q GLU* 3.8 5.6 - - - +
39Q MSE 1.3 75.2 - - - +
41Q LEU* 1.3 60.7 + - + +
44Q GLN* 2.7 75.5 + - - +
222V LEU* 4.2 23.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 41 (chain Q).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37Q GLU* 2.9 23.4 + - + +
38Q ILE* 4.0 2.5 - - - +
40Q GLN* 1.3 76.3 - - + +
42Q HIS* 1.3 59.5 + - - +
44Q GLN* 5.1 0.4 - - - +
45Q LYS* 2.9 46.8 + - + +
46Q HIS* 3.2 5.5 + - - -
180Q HIS 6.0 0.7 - - - +
184Q LEU* 3.3 34.1 - - + -
183S TYR* 4.0 17.9 - - - +
187S LYS* 4.0 21.8 - - + -
188S ASN* 3.3 25.4 - - - +
222V LEU* 6.2 4.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 42 (chain Q).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38Q ILE* 2.8 24.5 + - + +
39Q MSE 3.8 4.0 - - - +
41Q LEU* 1.3 79.1 - - - +
43Q HIS* 1.3 56.1 + - - +
46Q HIS* 3.3 15.0 - - + +
47Q HIS* 2.8 28.9 + - - +
90Q HIS* 2.6 31.2 + + - -
93Q PHE* 3.8 18.7 - + - -
94Q TRP* 3.6 16.5 - + + -
176Q ASP* 3.1 19.0 + - - -
180Q HIS* 3.4 25.0 + + - +
181Q ALA* 3.6 26.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 43 (chain Q).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20Q LEU* 3.5 38.6 - - + +
21Q PRO 2.6 29.0 + - - -
22Q PRO* 4.0 4.5 - - + -
23Q LEU* 3.6 29.1 + - + +
27Q TYR* 3.3 27.5 + - + -
39Q MSE 3.1 18.8 + - - +
42Q HIS* 1.3 75.4 - - - +
44Q GLN* 1.3 66.0 + - - +
47Q HIS* 3.5 4.1 - - - +
48Q GLN* 3.2 21.5 + - - +
94Q TRP* 3.7 29.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 44 (chain Q).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20Q LEU* 4.7 7.2 - - + -
27Q TYR* 3.4 25.6 + - - +
40Q GLN* 2.7 60.2 + - - +
43Q HIS* 1.3 75.1 - - - +
45Q LYS* 1.3 84.5 + - + +
48Q GLN* 3.0 22.7 - - - +
222V LEU* 5.9 0.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 45 (chain Q).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41Q LEU* 2.9 30.4 + - + +
44Q GLN* 1.3 103.1 + - + +
46Q HIS* 1.3 60.5 + - - +
48Q GLN* 4.0 0.3 - - - +
49Q GLY* 3.1 24.1 + - - -
188S ASN* 3.4 45.3 - - + +
221V LYS* 6.3 0.6 - - - +
----------------------------------------------------------
Back to top of page
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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
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