Contacts of the helix formed by residues 35 - 43 (chain K) in PDB entry 6T9L
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 35 (chain K).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33K HIS 4.3 0.4 + - - -
34K SER* 1.3 73.1 - - - +
36K PRO* 1.3 78.6 - - + +
37K LYS* 3.8 20.6 - - + +
38K GLU* 3.6 34.3 - - + +
39K LYS* 3.0 19.9 + - - +
42N THR* 5.3 7.4 + - + +
45N GLN* 5.0 3.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 36 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34K SER 3.8 5.8 - - - +
35K VAL* 1.3 92.1 - - + +
37K LYS* 1.3 62.2 + - + +
39K LYS* 3.5 16.4 + - + +
40K PHE* 3.1 36.4 - - + -
17L VAL* 4.6 0.2 - - - +
23L GLU* 5.8 7.4 - - + -
45N GLN* 4.3 14.4 - - + +
46N TYR 5.3 7.9 - - - +
47N ASP 6.1 1.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 37 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35K VAL* 3.1 18.0 - - + +
36K PRO* 1.3 81.7 - - + +
38K GLU* 1.3 72.0 + - - +
39K LYS 3.4 0.3 + - - -
40K PHE 3.8 3.3 + - - -
41K LEU* 3.6 19.8 - - + +
17L VAL* 3.7 35.9 - - + +
18L GLU* 4.8 9.6 - - - -
20L GLY* 5.8 5.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 38 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34K SER* 5.9 1.6 - - - -
35K VAL* 3.4 24.1 + - + +
37K LYS* 1.3 82.1 - - + +
39K LYS* 1.3 63.2 + - - +
40K PHE 3.3 0.4 - - - -
41K LEU* 3.6 25.0 - - - +
42K ASN* 3.0 48.0 + - - +
43K THR* 4.6 0.7 - - - +
35N LEU* 4.7 13.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 39 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31K LEU* 3.7 37.5 + - + +
34K SER* 4.8 15.0 - - - +
35K VAL 3.0 17.4 + - - +
36K PRO* 3.6 16.8 - - + +
37K LYS 3.2 1.0 - - - -
38K GLU* 1.3 77.7 - - - +
40K PHE* 1.3 65.6 + - + +
43K THR* 2.3 50.6 + - + +
44K MET* 3.1 25.2 + - + +
89K SER 4.5 2.3 + - - -
46N TYR 5.1 4.0 + - - -
47N ASP* 4.0 28.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 40 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36K PRO* 3.1 35.0 - - + -
37K LYS 3.8 2.6 + - - +
38K GLU 3.3 0.2 - - - -
39K LYS* 1.3 82.6 - - + +
41K LEU* 1.3 61.6 + - + +
44K MET* 3.3 40.4 - - + -
45K LYS* 3.1 28.1 + - - +
52K ILE* 3.5 20.2 - - + +
53K ASN* 3.7 9.2 - - - -
17L VAL* 4.3 15.7 - - + -
22L TYR* 3.5 43.5 - + + -
23L GLU* 5.6 7.6 - - + -
26L SER* 5.5 5.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 41 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37K LYS* 3.6 15.3 - - + +
38K GLU* 3.4 33.5 + - - +
39K LYS 3.4 0.4 - - - -
40K PHE* 1.3 81.4 - - + +
42K ASN* 1.3 64.3 + - - +
45K LYS* 3.4 48.8 + - - +
52K ILE* 4.9 6.1 - - + -
13L GLN 5.4 0.4 - - - +
14L GLN* 5.1 13.7 - - + -
17L VAL* 4.0 27.6 - - + -
18L GLU* 5.7 7.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 42 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38K GLU* 3.0 43.9 + - - +
41K LEU* 1.3 86.8 + - - +
43K THR* 1.3 64.6 + - + +
44K MET 3.7 0.4 - - - -
45K LYS* 4.6 4.3 - - - +
66K CYS* 3.7 20.1 - - - -
30N ASP* 4.9 17.6 + - - +
31N SER 5.8 1.5 + - - +
32N TRP* 4.9 13.9 + - - +
34N SER* 5.8 0.2 + - - -
35N LEU* 3.4 30.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 43 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30K ILE* 5.1 11.2 - - + -
31K LEU* 4.4 17.3 - - + +
34K SER* 5.2 4.0 - - - +
38K GLU 4.6 0.4 - - - +
39K LYS* 2.3 48.4 + - + +
42K ASN* 1.3 85.8 - - + +
44K MET* 1.3 63.9 + - - +
45K LYS 3.7 1.6 - - - -
57K THR* 3.5 14.8 - - - +
59K MET* 5.5 8.0 + - - +
66K CYS* 5.2 4.8 - - - -
89K SER* 3.6 25.8 + - - -
32N TRP* 5.8 7.0 - - + -
35N LEU* 5.3 5.2 - - + -
----------------------------------------------------------
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