Contacts of the helix formed by residues 19 - 31 (chain L) in PDB entry 5T0G
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 ILE 19 (chain L).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9L ASP 4.9 1.3 - - - +
10L VAL* 3.5 27.8 - - - +
11L THR 4.7 3.1 - - - +
12L VAL 3.5 20.2 - - - +
13L TRP* 4.4 37.0 - - + -
14L SER* 4.4 2.0 - - - -
17L GLY 4.0 1.2 + - - -
18L ARG* 1.3 70.1 - - - +
20L HIS* 1.3 64.8 + - - +
21L GLN* 3.2 19.9 + - + +
22L ILE* 3.5 35.0 + - + +
23L GLU* 3.8 12.1 + - - +
120L THR 5.4 3.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 20 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6L TYR* 3.6 17.1 + + - -
7L ASP* 2.5 37.0 + - + +
14L SER* 3.1 27.9 + - - -
18L ARG* 3.7 21.9 + - - -
19L ILE* 1.3 71.9 - - - +
21L GLN* 1.3 59.2 + - - +
22L ILE 3.3 0.2 - - - -
23L GLU* 3.3 27.3 + - - -
24L TYR* 2.9 66.4 + + + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 21 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10K ARG* 3.4 11.3 - - - +
14K THR* 3.1 24.5 - - - +
15K PHE* 3.9 22.6 + - + +
7L ASP* 2.3 36.4 + - - +
8L ASN 3.6 6.9 + - - -
9L ASP 3.8 15.2 + - - +
10L VAL* 3.8 26.0 - - + -
19L ILE* 3.2 10.4 - - + -
20L HIS* 1.3 79.1 - - - +
22L ILE* 1.3 58.0 + - + +
24L TYR* 3.4 8.8 + - - +
25L ALA* 3.0 26.3 + - - +
127L PRO* 4.4 11.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 22 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10L VAL* 4.7 6.7 - - + -
19L ILE* 3.5 34.5 + - + +
20L HIS 3.3 0.4 - - - -
21L GLN* 1.3 78.3 - - + +
23L GLU* 1.3 62.8 + - + +
25L ALA* 3.1 9.2 + - + +
26L MET* 2.9 54.3 + - + +
120L THR* 5.1 15.5 - - + +
127L PRO* 4.6 17.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 23 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18L ARG* 2.6 48.4 + - - +
19L ILE 3.8 14.7 + - - +
20L HIS* 3.3 25.8 + - - +
22L ILE* 1.3 79.5 - - + +
24L TYR* 1.3 63.0 + - + +
26L MET* 2.9 27.8 + - + +
27L GLU* 3.0 18.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 24 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10K ARG* 4.3 17.9 - - - -
15K PHE* 4.5 9.7 - - + -
16K SER 3.3 18.6 - - - +
17K PRO* 3.1 46.0 - - + +
19K GLY* 4.1 11.1 + - - +
7L ASP* 3.4 19.4 + - + -
20L HIS* 2.9 51.8 + + + +
21L GLN* 3.7 15.7 - - - +
23L GLU* 1.3 79.5 - - + +
25L ALA* 1.3 60.1 + - - +
27L GLU* 3.5 21.8 + - + +
28L ALA* 3.5 4.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 25 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15K PHE* 3.7 29.3 - - + -
21L GLN 3.0 11.0 + - - +
22L ILE* 3.1 12.1 + - + +
24L TYR* 1.3 76.1 - - - +
26L MET* 1.3 60.4 + - + +
28L ALA* 2.8 25.8 + - - +
29L VAL* 3.0 15.4 + - + +
127L PRO* 4.8 6.5 - - + -
128L TYR 5.1 2.2 - - - +
129L GLY* 4.8 12.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 26 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22L ILE* 2.9 38.2 + - + +
23L GLU* 2.9 16.9 + - + +
25L ALA* 1.3 74.4 - - + +
27L GLU* 1.3 57.6 + - - +
29L VAL* 3.1 17.7 + - - +
30L LYS* 3.0 46.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 27 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17K PRO 4.6 4.0 - - - +
18K GLU 3.2 28.4 - - - +
19K GLY 5.2 0.4 - - - -
23L GLU* 3.0 14.5 + - - +
24L TYR* 3.5 15.5 - - + +
25L ALA 3.1 0.2 - - - -
26L MET* 1.3 78.0 - - - +
28L ALA* 1.3 61.0 + - - +
30L LYS* 3.1 27.8 + - - +
31L GLN* 3.0 30.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 28 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19K GLY 4.3 17.2 + - - +
20K ARG* 6.0 0.9 - - - -
24L TYR 3.5 4.1 + - - +
25L ALA* 2.8 17.1 + - - +
27L GLU* 1.3 77.1 - - - +
29L VAL* 1.3 63.8 + - + +
31L GLN* 3.1 17.8 + - - +
32L GLY 3.4 7.4 + - - -
76L GLY* 4.2 17.4 - - - -
77L LEU* 5.5 9.9 - - + -
129L GLY* 5.3 8.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 29 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25L ALA 3.0 13.8 + - - +
26L MET* 3.1 20.6 + - - +
28L ALA* 1.3 76.8 - - - +
30L LYS* 1.3 63.2 + - + +
32L GLY* 3.3 14.0 + - - +
75L ALA* 4.9 8.2 - - + +
76L GLY* 5.4 5.2 - - - +
129L GLY* 5.0 2.0 - - - -
130L VAL* 3.4 37.2 - - + +
131L GLY* 5.1 7.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 30 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26L MET* 3.0 35.9 + - - +
27L GLU* 3.1 30.1 + - - +
29L VAL* 1.3 77.9 - - + +
31L GLN* 1.3 63.1 + - + +
32L GLY 3.2 7.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 31 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18K GLU 5.6 4.8 + - - +
19K GLY 6.1 1.8 - - - +
20K ARG* 5.6 10.1 - - - +
27L GLU* 3.0 22.4 + - + +
28L ALA* 3.1 11.8 + - - +
30L LYS* 1.3 75.7 - - + +
32L GLY* 1.3 58.7 + - - +
51L ARG* 3.1 22.7 + - - -
76L GLY* 6.0 0.2 - - - -
----------------------------------------------------------
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