Contacts of the helix formed by residues 26 - 37 (chain U) in PDB entry 6L49
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 PRO 26 (chain U).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18U SER* 3.3 16.2 - - - +
24U GLN 3.7 0.6 - - - +
25U PHE* 1.3 88.2 - - + +
27U VAL* 1.3 62.7 + - - +
28U GLY 4.3 1.1 - - - +
29U ARG* 3.7 37.5 - - + +
30U VAL* 3.3 19.5 - - + +
52U ALA* 3.9 4.9 - - - +
34V TYR* 3.8 20.2 - - + +
37V TYR* 3.4 40.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 27 (chain U).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17U ARG* 3.4 52.3 - - + +
18U SER* 3.7 7.4 + - - -
21U ALA* 3.8 20.9 - - + -
23U LEU* 5.2 2.7 - - + -
25U PHE 3.7 3.5 + - - +
26U PRO* 1.3 72.8 - - - +
28U GLY* 1.3 60.0 + - - +
29U ARG 3.4 0.2 - - - -
30U VAL 3.6 0.9 + - - -
31U HIS* 2.9 29.1 + - - +
45U ALA 4.7 0.2 - - - +
48U PRO* 3.3 19.3 - - + +
49U VAL* 3.8 30.5 - - + -
52U ALA* 5.4 0.2 - - + -
118V TYR* 4.3 7.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 28 (chain U).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126I A 3.4 34.0 + - - +
127I T 3.8 6.8 + - - -
17U ARG* 3.7 20.0 - - - -
26U PRO* 3.4 2.2 - - - +
27U VAL* 1.3 78.1 - - - +
29U ARG* 1.3 59.6 + - - +
31U HIS* 3.6 1.1 - - - +
32U ARG* 2.9 25.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 29 (chain U).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125I A 5.1 3.4 + - - -
126I A 3.3 39.1 + - - +
127I T 5.6 1.0 + - - -
-124J G 5.5 7.5 - - - +
-123J A 5.9 1.0 + - - -
-122J G 3.6 33.4 + - - -
16U THR* 5.9 4.4 - - - +
26U PRO* 3.7 30.6 - - + +
27U VAL 3.4 0.2 - - - -
28U GLY* 1.3 76.4 - - - +
30U VAL* 1.3 57.3 + - - +
32U ARG* 3.3 6.9 + - - +
33U LEU* 2.9 35.6 + - + +
30V ARG* 5.5 2.2 - - - +
32V GLU* 3.4 41.1 + - + +
34V TYR* 4.6 7.9 - - + +
37V TYR* 3.6 21.2 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 30 (chain U).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25U PHE* 6.0 0.7 - - + -
26U PRO* 3.3 20.6 - - + +
27U VAL 3.6 0.6 + - - -
28U GLY 3.4 0.2 - - - -
29U ARG* 1.3 75.3 - - + +
31U HIS* 1.3 57.1 + - - +
33U LEU* 3.4 7.3 + - + +
34U LEU* 2.9 29.4 + - + +
48U PRO* 3.7 30.5 - - + +
51U LEU* 3.8 17.7 - - + -
52U ALA* 4.7 8.1 - - + +
55U LEU* 5.3 4.9 - - + -
34V TYR* 3.7 21.3 - - + +
67V PHE* 3.6 27.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 31 (chain U).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
-131J A 3.5 17.0 + - - -
17U ARG* 3.3 34.3 + - - +
27U VAL 2.9 18.6 + - - +
28U GLY 3.6 4.9 - - - +
29U ARG 3.2 0.2 - - - -
30U VAL* 1.3 76.6 - - - +
32U ARG* 1.3 56.4 + - - +
34U LEU* 3.3 5.2 + - - +
35U ARG* 2.9 78.5 + - + +
43U VAL* 3.7 13.7 - - + -
44U GLY 4.0 7.9 - - - -
45U ALA* 4.3 10.7 - - - +
48U PRO* 3.4 21.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 32 (chain U).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125I A 3.9 14.7 - - - -
126I A 3.2 40.7 + - - +
28U GLY 2.9 8.3 + - - +
29U ARG* 3.7 11.9 + - - +
31U HIS* 1.3 76.6 - - - +
33U LEU* 1.3 91.6 + - - +
35U ARG* 4.4 5.8 - - - +
36U LYS* 2.9 63.4 + - + +
32V GLU* 2.7 40.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 33 (chain U).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29U ARG* 2.9 24.3 + - + +
30U VAL* 3.8 3.8 - - + +
31U HIS 3.3 0.2 - - - -
32U ARG* 1.3 99.8 - - - +
34U LEU* 1.3 58.5 + - - +
36U LYS* 5.3 0.9 - - + -
37U GLY* 3.1 20.9 + - - +
39U TYR* 3.2 15.6 - - - -
34V TYR* 4.8 13.9 - - + +
64V ASN* 5.5 5.4 - - - +
67V PHE* 3.6 35.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 34 (chain U).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30U VAL 2.9 20.6 + - - +
31U HIS* 3.8 5.6 - - - +
32U ARG 3.2 0.2 - - - -
33U LEU* 1.3 78.0 - - - +
35U ARG* 1.3 62.4 + - - +
37U GLY 4.0 1.8 + - - -
39U TYR* 3.6 42.2 + - + +
40U SER 5.0 1.4 + - - +
43U VAL* 3.7 42.1 - - + +
47U ALA* 4.1 2.2 - - + -
48U PRO* 3.8 33.4 - - + -
51U LEU* 3.8 28.0 - - + -
67V PHE* 4.6 3.4 - - + -
71V ALA* 4.4 8.1 - - + -
75V SER* 5.5 0.9 - - - +
86V ILE* 5.5 2.2 - - + -
91V ILE* 5.2 4.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 35 (chain U).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127I T 6.0 4.4 - - - +
128I T 5.5 10.5 + - - +
-132J G 4.6 1.4 - - - +
-131J A 2.8 83.1 + - - +
-130J C 4.3 23.0 - - - +
17U ARG* 5.9 0.6 - - - +
31U HIS* 2.9 48.7 + - + +
32U ARG* 4.0 5.4 - - - +
34U LEU* 1.3 79.3 - - + +
36U LYS* 1.3 63.3 + - + +
37U GLY 3.5 0.2 - - - -
38U ASN* 4.5 4.5 + - - -
40U SER 5.4 3.6 - - - +
43U VAL* 5.2 2.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 36 (chain U).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125I A 5.7 4.9 + - - +
126I A 5.0 2.2 + - - -
32U ARG* 2.9 44.5 + - + +
33U LEU* 5.3 0.9 - - + -
35U ARG* 1.3 80.3 - - + +
37U GLY* 1.3 56.4 + - - +
38U ASN* 3.2 23.5 + - - -
41Y GLU* 5.2 9.2 - - - +
79Z HIS* 4.5 1.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 37 (chain U).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33U LEU* 3.1 23.7 + - - -
34U LEU 4.0 0.8 + - - -
35U ARG 3.5 1.0 - - - -
36U LYS* 1.3 76.1 - - - +
38U ASN* 1.3 70.9 + - - +
39U TYR* 3.4 18.3 + - - -
79Z HIS* 3.2 22.3 + - - -
----------------------------------------------------------
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