Contacts of the helix formed by residues 26 - 38 (chain A) in PDB entry 3HPD
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 26 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22A THR* 3.2 27.6 - - - +
23A ASN* 3.0 28.5 + - - +
25A VAL* 1.3 88.8 - - + +
27A MET* 1.3 57.9 + - - +
28A ASN 3.4 2.0 - - - -
29A THR* 3.7 13.0 - - + -
30A THR* 2.8 53.1 + - + +
191A THR 5.0 0.9 - - - +
192A GLY* 3.9 27.8 - - - -
195A CYS* 4.0 10.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 27 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22A THR* 3.5 35.7 - - + +
23A ASN 3.3 12.0 + - - +
24A PHE* 4.0 26.2 + - + +
25A VAL 3.6 1.6 - - - -
26A VAL* 1.3 79.0 - - - +
28A ASN* 1.3 61.3 + - - +
30A THR* 4.4 1.6 - - - -
31A ALA* 3.4 20.3 + - - +
43A MET* 3.5 37.5 - - + +
71A TRP* 3.7 23.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 28 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25A VAL 5.4 0.4 + - - -
27A MET* 1.3 77.3 - - - +
29A THR* 1.3 62.5 + - - +
31A ALA* 3.3 6.0 + - - +
32A ASN* 2.9 56.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 29 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25A VAL 4.6 4.7 - - - +
26A VAL* 3.6 32.1 - - + +
28A ASN* 1.3 82.0 - - - +
30A THR* 1.3 65.2 + - + +
33A ALA* 3.0 24.3 + - - +
191A THR* 4.9 5.4 + - + +
192A GLY 4.7 1.6 - - - +
196A MET* 3.8 19.3 - - + +
239A HIS* 3.5 16.5 + - - -
243A TYR* 2.9 30.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 30 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20A ASN* 4.4 2.5 + - - -
22A THR* 4.5 3.8 + - - +
26A VAL* 2.8 49.8 + - + +
27A MET* 4.4 0.2 - - - -
29A THR* 1.3 77.5 - - + +
31A ALA* 1.3 66.8 + - - +
33A ALA* 3.6 7.8 - - - +
34A LEU* 3.0 28.3 + - - +
43A MET* 3.3 19.3 - - - +
63A ASN* 5.8 0.2 - - - +
195A CYS* 3.7 29.2 - - + +
196A MET* 4.1 3.4 - - - -
199A ALA* 3.8 15.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 31 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27A MET 3.4 16.9 + - - +
28A ASN* 3.3 8.0 + - - +
30A THR* 1.3 82.4 + - - +
32A ASN* 1.3 60.3 + - - +
34A LEU* 3.3 1.7 + - - +
35A LEU* 3.0 32.8 + - + +
41A PRO* 3.6 27.9 - - + +
43A MET* 3.9 11.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 32 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28A ASN* 2.9 45.6 + - - +
31A ALA* 1.3 75.3 - - - +
33A ALA* 1.3 60.6 + - - +
35A LEU* 3.9 18.6 - - - +
36A ALA* 3.0 29.3 + - - +
243A TYR* 3.8 24.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 33 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29A THR 3.0 18.7 + - - +
30A THR* 3.6 9.6 - - - +
31A ALA 3.2 0.2 - - - -
32A ASN* 1.3 75.0 - - - +
34A LEU* 1.3 63.4 + - - +
36A ALA* 3.4 3.5 + - - +
37A LEU* 3.1 23.2 + - - +
196A MET* 4.5 18.6 - - + +
199A ALA* 5.7 0.7 - - + -
200A LEU* 3.6 13.4 - - + +
243A TYR* 3.7 13.7 - - + -
246A LEU* 3.9 20.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 34 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18A VAL* 4.0 13.9 - - + -
20A ASN* 3.7 27.6 - - - +
30A THR 3.0 19.0 + - - +
31A ALA 3.6 4.7 - - - +
33A ALA* 1.3 76.9 - - - +
35A LEU* 1.3 60.6 + - - +
37A LEU* 3.3 3.6 + - + +
38A GLY 3.1 5.7 + - - -
39A ALA* 2.9 35.6 + - + +
41A PRO* 3.7 22.4 - - + -
199A ALA* 3.3 37.0 - - + +
200A LEU* 4.2 8.5 - - + -
203A ALA* 3.8 24.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 35 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31A ALA* 3.0 20.3 + - + +
32A ASN* 3.9 22.9 - - - +
33A ALA 3.3 0.2 - - - -
34A LEU* 1.3 77.1 - - - +
36A ALA* 1.3 64.3 + - - +
38A GLY* 3.2 12.5 + - - -
39A ALA 3.5 10.8 - - - +
40A SER* 4.4 4.5 - - - +
41A PRO* 3.5 26.0 - - + -
247A TYR* 5.3 2.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 36 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12A ARG* 4.8 0.5 + - - -
32A ASN 3.0 18.1 + - - +
33A ALA 3.7 4.7 - - - +
35A LEU* 1.3 78.5 - - - +
37A LEU* 1.3 61.7 + - - +
38A GLY* 3.4 0.9 + - - -
243A TYR* 3.3 35.2 - - + +
246A LEU* 3.9 10.1 - - + -
247A TYR* 3.1 36.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 37 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8A LEU* 3.7 26.7 - - + -
11A VAL* 4.0 21.5 - - + -
12A ARG* 3.0 31.2 + - - +
33A ALA 3.1 16.4 + - - +
34A LEU* 3.6 5.6 - - + +
36A ALA* 1.3 77.5 - - - +
38A GLY* 1.3 57.4 + - - +
39A ALA* 5.1 0.7 - - + -
200A LEU* 3.7 20.6 - - + -
203A ALA* 4.1 13.9 - - + -
204A PHE* 3.8 22.0 - - + -
220A THR* 4.0 20.9 - - + -
246A LEU* 3.6 20.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 38 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11A VAL* 3.8 7.0 - - - +
12A ARG* 4.4 0.9 - - - -
15A ARG* 2.3 57.9 + - - -
34A LEU 3.1 2.2 + - - -
35A LEU 3.2 10.3 + - - -
36A ALA 4.4 0.2 - - - -
37A LEU* 1.3 81.4 - - - +
39A ALA* 1.3 62.3 + - - +
----------------------------------------------------------
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