Contacts of the strand formed by residues 31 - 39 (chain H) in PDB entry 5UK7
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 LYS 31 (chain H).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23H SER* 4.0 18.2 + - - -
24H ILE 3.4 9.2 - - - +
25H TYR* 3.1 39.6 + - + -
29H GLY 3.5 2.9 + - - +
30H ILE* 1.3 77.4 - - - +
32H LEU* 1.3 75.6 + - - +
33H GLN* 3.7 34.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 32 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61G THR* 3.8 29.4 - - + -
22H VAL 3.7 0.5 - - - +
23H SER* 3.4 4.3 - - - -
24H ILE* 2.9 42.9 + - + +
26H LEU* 4.3 19.3 - - + -
30H ILE* 3.8 18.6 - - + -
31H LYS* 1.3 83.3 - - - +
33H GLN* 1.3 62.3 + - - +
46H LEU* 3.5 16.1 - - + +
52H GLN* 4.2 17.9 - - - +
54H VAL* 3.9 16.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 33 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22H VAL 3.4 6.7 - - - +
23H SER* 4.2 9.2 - - - +
31H LYS* 3.7 31.2 + - + +
32H LEU* 1.3 78.6 - - - +
34H GLY* 1.3 58.8 + - - +
46H LEU* 3.4 15.7 - - - +
48H ASN* 3.6 19.5 + - - +
52H GLN* 5.3 0.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 34 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21H PRO* 3.7 4.5 - - - +
22H VAL* 3.0 32.1 + - - +
33H GLN* 1.3 77.9 - - - +
35H GLN* 1.3 67.8 + - - -
46H LEU* 3.7 8.7 - - - +
47H LYS 3.3 13.7 - - - -
48H ASN* 4.2 4.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 35 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19H ARG* 3.5 50.1 - - + +
20H VAL 4.1 8.3 - - - +
21H PRO* 4.2 10.4 - - + +
34H GLY* 1.3 80.2 - - - +
36H ILE* 1.3 69.0 + - - +
37H GLU 3.2 1.0 + - - -
45H LEU 3.7 0.5 - - - +
46H LEU* 3.8 5.0 - - - +
47H LYS* 2.8 47.6 + - + +
48H ASN* 6.0 0.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 36 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12H LEU* 4.2 19.7 - - + +
15H LEU* 4.3 22.9 + - + +
16H ARG* 3.1 43.6 - - + +
19H ARG* 5.8 1.7 + - - +
20H VAL 4.9 1.6 + - - -
22H VAL* 3.9 27.1 - - + +
24H ILE* 4.6 8.7 - - + -
35H GLN* 1.3 75.5 - - - +
37H GLU* 1.3 58.9 + - - +
38H SER 3.7 21.1 - - - +
39H PHE* 4.4 7.6 - - + -
44H ILE* 3.7 24.9 - - + -
45H LEU 3.8 2.9 - - - -
46H LEU* 4.7 1.3 - - + -
62H VAL* 5.2 2.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 37 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16H ARG* 3.3 17.9 + - - +
35H GLN 3.2 0.8 + - - -
36H ILE* 1.3 74.3 - - - +
38H SER* 1.3 72.6 + - - +
45H LEU* 2.9 26.8 + - + +
47H LYS* 3.3 46.8 + - + +
51H SER* 3.4 12.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 38 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7G LEU* 3.6 28.9 - - - +
16H ARG* 4.3 11.5 + - - +
36H ILE* 3.6 8.6 - - - +
37H GLU* 1.3 93.3 + - - +
39H PHE* 1.3 69.6 + - - +
44H ILE* 3.7 0.2 - - - -
45H LEU* 2.9 28.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 39 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2G ALA* 3.3 32.7 + - + -
7G LEU* 3.7 6.5 - - - -
9H ASP* 3.6 32.3 - - - -
12H LEU* 3.6 38.4 - - + -
13H ASN* 3.1 44.4 - - - -
16H ARG* 4.8 10.2 - - - +
36H ILE* 4.4 9.0 - - + -
38H SER* 1.3 82.2 - - - +
40H ASP* 1.3 67.6 + - - +
43H VAL 3.4 13.5 - - - +
44H ILE* 4.1 15.3 - - + -
56H LYS* 4.4 2.9 - - - -
----------------------------------------------------------
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