Contacts of the strand formed by residues 38 - 46 (chain c) in PDB entry 5Z58
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 THR 38 (chain c).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31c GLY 3.4 4.7 - - - -
32c VAL* 4.4 7.2 - - - +
36c MET 3.2 8.2 + - - -
37c ASN* 1.3 73.7 - - - +
39c HIS* 1.3 60.9 + - - +
40c LEU* 5.8 0.2 - - - -
58c LEU 3.9 0.9 - - - +
59c SER* 3.5 2.0 - - - -
60c ILE* 2.7 48.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 39 (chain c).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8b LYS* 4.9 17.5 - - + -
29c ILE* 3.5 6.4 - - - +
30c THR* 2.8 34.2 + - - -
31c GLY* 2.7 23.5 + - - +
38c THR* 1.3 77.1 - - - +
40c LEU* 1.3 57.0 - - - +
58c LEU 3.4 6.1 - - - +
59c SER* 4.4 8.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 40 (chain c).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27c GLY* 4.5 7.9 - - - -
28c THR 3.1 21.8 - - - +
29c ILE* 4.7 1.1 - - - -
30c THR* 4.0 5.7 - - - +
39c HIS* 1.3 77.0 - - - +
41c LYS* 1.3 64.4 + - - +
43c VAL* 5.0 6.5 - - + -
57c THR* 3.4 7.8 - - - -
58c LEU* 2.8 35.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 41 (chain c).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118C PHE* 6.2 5.2 - - + -
121C ASP* 5.5 6.5 - - - +
27c GLY* 3.7 0.9 - - - -
28c THR* 2.8 36.6 + - - +
30c THR* 5.3 6.5 - - - -
40c LEU* 1.3 75.7 - - - +
42c ALA* 1.3 75.1 + - + +
43c VAL* 3.3 2.9 - - - -
56c GLU 3.2 13.2 - - - +
57c THR* 4.5 1.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 42 (chain c).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26c HIS 3.8 1.6 - - - +
27c GLY* 3.6 10.6 - - - -
28c THR* 4.3 5.5 + - - -
41c LYS* 1.3 78.2 - - + +
43c VAL* 1.3 60.3 + - - +
44c LYS 4.0 0.5 + - - -
55c LEU 3.8 3.6 - - - -
56c GLU* 3.1 13.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 43 (chain c).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25c VAL* 6.4 1.6 - - + -
26c HIS 3.3 9.2 - - - +
27c GLY* 4.1 4.7 - - - -
40c LEU* 5.0 4.7 - - + -
41c LYS 4.6 6.3 - - - +
42c ALA* 1.3 73.4 - - - +
44c LYS* 1.3 61.3 + - - +
45c MET* 3.9 5.6 + - + +
53c VAL 3.6 1.2 - - - +
54c GLN* 3.2 6.6 - - - +
55c LEU* 2.7 53.9 + - + +
58c LEU* 4.4 20.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 44 (chain c).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24c GLN 4.1 1.4 - - - +
25c VAL* 3.9 0.5 - - - -
26c HIS* 2.8 41.5 + - + +
42c ALA 4.0 1.6 + - - -
43c VAL* 1.3 70.8 - - - +
45c MET* 1.3 59.9 + - - +
46c THR* 4.2 1.1 + - - -
52c PRO* 4.9 12.8 - - + -
53c VAL 3.5 7.0 - - - +
54c GLN* 4.5 5.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 45 (chain c).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24c GLN 3.4 6.7 - - - +
25c VAL* 4.4 9.9 - - + +
43c VAL* 3.9 7.2 - - + +
44c LYS* 1.3 74.0 - - - +
46c THR* 1.3 61.6 + - - +
47c LEU 3.9 2.3 + - - -
51c GLU 4.7 0.3 - - - +
52c PRO* 3.5 1.3 - - - +
53c VAL* 2.9 42.8 + - + +
55c LEU* 6.2 2.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 46 (chain c).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22c GLY 4.9 0.2 - - - +
23c THR* 4.6 1.1 - - - -
24c GLN* 2.7 45.1 + - - +
44c LYS 4.2 1.0 + - - -
45c MET* 1.3 71.7 - - - +
47c LEU* 1.3 69.8 + - - +
48c LYS* 3.5 1.2 + - - -
50c ARG 4.6 5.8 - - - -
51c GLU 5.1 0.9 - - - -
52c PRO* 4.2 20.9 - - - -
----------------------------------------------------------
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