Contacts of the strand formed by residues 40 - 47 (chain H) in PDB entry 2QC8
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 LEU 40 (chain H).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31H ILE* 3.8 17.7 - - + -
32H TRP* 3.3 12.6 - - - +
33H ILE* 4.1 11.4 - - + -
38H GLU 3.7 2.6 + - - +
39H GLY* 1.3 75.1 - - - -
41H ARG* 1.3 67.4 + - - +
98H LEU* 5.0 4.5 - - + -
219H TRP* 3.9 40.4 - - + +
222H ARG* 4.1 7.2 - - + -
223H PHE* 3.7 39.3 - - + +
226H HIS* 4.3 11.6 - - + +
163I CYS 4.2 1.4 - - - +
164I GLY* 4.7 0.3 - - - -
165I VAL* 3.5 31.7 + - + +
169I ARG* 6.0 1.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 41 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31H ILE* 3.3 5.5 - - - +
32H TRP* 2.8 61.5 + - + +
34H ASP* 2.9 44.2 + - + +
36H THR* 5.3 4.2 - - - +
40H LEU* 1.3 79.0 + - - +
42H CYS* 1.3 66.7 + - - +
66H SER 3.7 7.7 + - - -
67H THR* 3.9 23.0 + - + +
223H PHE* 5.0 1.1 - - - -
159I GLY 3.1 28.5 + - - -
160I PRO* 3.6 19.7 - - - +
162I TYR* 2.7 37.6 + - - +
163I CYS* 3.0 11.4 - - + +
164I GLY* 4.6 2.0 - - - +
165I VAL* 5.1 0.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 42 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29H MET* 3.4 35.2 - - + -
30H TYR 3.0 17.7 - - - +
31H ILE* 4.0 2.5 - - + -
32H TRP* 3.5 7.4 - - - -
41H ARG* 1.3 78.1 - - - +
43H LYS* 1.3 62.0 + - - +
223H PHE* 3.6 22.9 - - + -
163I CYS* 2.9 33.0 + - - +
164I GLY 4.7 6.7 - - - -
165I VAL* 4.9 2.5 - - - -
173I ARG* 4.7 11.4 - - - -
194I ASN* 5.0 1.0 - - - +
195I ALA 5.3 0.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 43 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29H MET* 4.2 1.1 - - - -
30H TYR* 2.8 31.3 + - - +
32H TRP* 4.0 11.4 - - + -
42H CYS* 1.3 79.7 - - - +
44H THR* 1.3 59.1 + - - +
60H TRP* 3.2 48.0 - - + +
61H ASN* 2.9 31.0 + - - +
62H PHE* 4.2 16.5 - - - +
79H LEU* 4.6 1.8 - - - -
162I TYR* 5.0 3.7 + - - +
163I CYS* 3.8 5.6 - - - -
193I THR 3.6 9.9 - - - +
194I ASN* 3.6 23.1 - - + +
205I GLN* 6.2 0.4 - - - +
501I ADP 4.9 12.1 + - - -
709I CL 3.7 11.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 44 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27H GLN* 3.8 7.6 - - + -
28H ALA 3.3 11.0 - - - +
29H MET* 3.2 9.2 - - - +
43H LYS* 1.3 74.4 - - - +
45H ARG* 1.3 68.3 + - - +
60H TRP* 3.5 10.6 - - - -
90H ARG* 2.9 37.0 + - - +
180I TYR* 3.6 21.1 - - + +
192I GLY* 3.1 3.4 - - - -
193I THR* 3.0 34.1 + - - +
205I GLN* 4.5 0.5 - - - +
709I CL 2.9 20.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 45 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27H GLN* 3.5 2.8 - - - -
28H ALA* 2.9 38.3 + - + +
30H TYR* 3.8 21.4 + - + -
44H THR* 1.3 74.3 - - - +
46H THR* 1.3 64.0 + - - +
47H LEU* 3.7 23.2 - - + +
58H PRO* 3.4 28.2 - - - +
59H GLU 3.5 17.8 + - - -
60H TRP* 3.5 44.5 - - + +
180I TYR* 3.3 6.1 - - - -
191I ALA 3.3 10.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 46 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25H LYS* 3.5 39.0 - - + -
26H VAL 3.3 7.6 - - - +
27H GLN* 4.7 0.4 - - + +
45H ARG* 1.3 76.6 + - - +
47H LEU* 1.3 72.2 + - - +
180I TYR* 2.7 25.6 + - + -
184I LEU* 4.3 5.4 - - + -
190I ILE 2.7 27.2 + - - +
191I ALA* 2.8 15.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 47 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25H LYS* 3.4 4.7 - - - +
26H VAL* 2.6 42.6 + - + +
28H ALA* 4.1 12.3 - - + -
45H ARG* 3.7 28.3 - - + +
46H THR* 1.3 85.5 - - - +
48H ASP* 1.3 62.4 + - - +
49H SER 3.2 12.8 - - - +
51H PRO* 4.0 20.0 - - + -
57H LEU* 3.5 31.4 - - + -
58H PRO* 4.5 16.2 - - + -
----------------------------------------------------------
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