Contacts of the helix formed by residues 19 - 31 (chain A) in PDB entry 3PJF
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 19 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13A GLY 3.6 14.8 + - - -
14A VAL* 4.2 1.3 - - - -
15A ALA 2.9 22.2 + - - -
16A SER* 3.0 18.9 + - - -
18A LEU* 1.3 81.7 - - - +
20A ILE* 1.3 65.7 + - - +
21A ALA 4.0 4.5 - - - -
22A TYR* 3.0 22.3 + - - +
23A GLY 3.3 4.2 + - - -
222A ILE* 4.0 4.0 - - - +
501A NAD 2.6 28.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 20 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18A LEU 3.5 0.9 + - - +
19A SER* 1.3 72.5 - - - +
21A ALA* 1.3 52.0 + - - +
23A GLY* 3.0 3.1 + - - -
24A ILE* 2.8 37.0 + - + +
144A LEU* 3.3 27.6 - - + -
189A ALA* 4.4 11.9 - - + -
192A ILE* 3.5 31.0 - - + -
222A ILE* 3.9 9.2 - - + +
225A VAL* 3.4 25.8 - - + -
501A NAD 2.8 59.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 21 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11A VAL* 3.8 8.5 - - + +
12A THR 3.1 28.7 - - - +
13A GLY 3.7 19.5 - - - +
14A VAL* 3.8 8.1 - - + -
19A SER* 4.5 0.2 - - - -
20A ILE* 1.3 80.2 - - - +
22A TYR* 1.3 55.1 + - - +
24A ILE* 3.6 11.6 - - - +
25A ALA* 2.8 30.8 + - - +
89A VAL* 5.4 0.2 - - + -
91A SER* 3.9 12.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 22 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14A VAL* 4.3 10.0 - - + +
16A SER 3.6 17.7 - - - +
17A LYS* 3.3 35.7 - - + +
19A SER* 3.0 14.7 + - - +
21A ALA* 1.3 78.4 - - - +
23A GLY* 1.3 64.5 + - - +
25A ALA* 3.4 7.2 + - + +
26A GLN* 2.9 74.1 + - + +
51A PHE* 3.3 61.8 - + + -
54A GLN* 4.6 5.5 + - - -
55A LEU* 6.3 2.5 - - + -
222A ILE* 4.7 1.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 23 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19A SER 3.3 4.4 + - - -
20A ILE 3.0 6.2 + - - -
22A TYR* 1.3 80.6 - - - +
24A ILE* 1.3 62.3 + - - +
26A GLN* 3.5 9.9 + - - +
27A ALA* 3.2 22.0 + - - +
222A ILE* 3.7 37.1 - - - +
223A GLU* 5.0 3.5 - - - -
226A GLY* 3.8 2.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 24 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11A VAL* 5.2 2.2 - - + -
20A ILE* 2.8 40.8 + - + +
21A ALA* 3.6 8.5 - - - +
23A GLY* 1.3 75.4 - - - +
25A ALA* 1.3 66.4 + - - +
27A ALA* 3.1 3.6 + - - +
28A MET* 3.0 45.0 + - + +
89A VAL* 3.8 29.6 - - + -
142A LEU* 4.9 1.3 - - + -
144A LEU* 4.4 11.4 - - + -
225A VAL* 4.5 4.0 - - + +
226A GLY* 3.8 13.0 - - - -
229A ALA* 3.6 31.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 25 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11A VAL* 4.4 8.9 - - + +
14A VAL* 5.3 0.7 - - + -
21A ALA 2.8 22.3 + - - +
22A TYR* 3.8 7.4 - - + +
24A ILE* 1.3 74.7 - - - +
26A GLN* 1.3 63.6 + - - +
28A MET* 3.4 2.9 + - - +
29A HIS* 3.0 26.2 + - - +
35A LEU* 3.5 12.2 - - + +
37A PHE* 3.8 29.6 - - + -
55A LEU* 3.9 11.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 26 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22A TYR* 2.9 63.3 + - + +
23A GLY* 3.8 11.1 - - - +
25A ALA* 1.3 77.7 - - + +
27A ALA* 1.3 58.9 + - - +
29A HIS* 3.8 6.3 + - - +
30A ARG* 3.0 28.6 + - - +
55A LEU* 4.8 15.6 - - + +
222A ILE* 4.9 1.6 - - - +
223A GLU* 4.5 11.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 27 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23A GLY 3.2 9.6 + - - +
24A ILE 3.1 6.8 + - - +
26A GLN* 1.3 74.9 - - - +
28A MET* 1.3 64.6 + - - +
30A ARG* 3.1 18.2 + - - +
31A GLU* 3.0 24.6 + - - +
223A GLU 5.5 0.4 - - - +
226A GLY 3.3 34.8 - - - +
227A ASN* 4.0 12.8 - - - +
230A ALA* 4.3 7.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 28 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4A LEU* 3.7 21.8 - - + -
9A ILE* 3.6 27.4 - - + -
11A VAL* 4.4 4.9 - - - -
24A ILE* 3.0 28.8 + - + +
25A ALA 3.9 2.9 - - - +
27A ALA* 1.3 75.2 - - - +
29A HIS* 1.3 61.2 + - - +
31A GLU* 3.1 9.0 + - - +
32A GLY 3.2 0.2 + - - -
33A ALA* 2.9 32.3 + - + +
35A LEU* 4.1 11.2 - - + -
89A VAL* 3.6 15.5 - - + -
229A ALA 4.0 9.6 - - - +
230A ALA* 4.2 8.1 - - + -
233A CYS* 3.5 41.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 29 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25A ALA 3.0 19.0 + - - +
26A GLN 3.8 4.3 + - - +
28A MET* 1.3 74.1 - - - +
30A ARG* 1.3 68.8 + - - +
32A GLY* 3.0 14.4 + - - -
33A ALA 4.1 16.8 - - - -
35A LEU* 4.1 8.7 - - + +
54A GLN 5.0 2.7 - - - -
55A LEU* 3.3 58.5 + - + +
56A GLY* 5.2 0.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 30 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2A GLY* 4.8 2.6 - - - -
3A PHE* 4.9 5.3 - - - -
26A GLN 3.0 15.4 + - - +
27A ALA* 3.1 24.1 + - - +
29A HIS* 1.3 79.4 - - - +
31A GLU* 1.3 92.5 + - - +
32A GLY 3.5 2.3 + - - -
227A ASN* 2.6 36.1 + - - +
230A ALA* 5.6 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 31 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2A GLY* 2.9 23.8 - - - -
3A PHE* 2.9 57.5 + - + -
4A LEU* 2.9 39.4 + - + +
5A SER 3.2 1.6 + - - -
27A ALA 3.0 15.8 + - - +
28A MET 3.1 8.5 + - - +
29A HIS 3.0 0.6 - - - -
30A ARG* 1.3 106.3 + - - +
32A GLY* 1.3 56.5 + - - +
33A ALA 3.5 0.2 - - - -
230A ALA* 4.7 1.1 - - + -
----------------------------------------------------------
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