Contacts of the strand formed by residues 45 - 53 (chain D) in PDB entry 6CP3
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 45 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38D GLU* 3.5 35.5 + - + +
39D ILE 3.5 11.9 - - - +
40D LYS* 4.6 6.3 - - + +
41D THR* 4.8 0.2 - - - -
44D GLY* 1.3 74.8 - - - -
46D LEU* 1.3 61.0 + - - +
47D VAL* 3.8 25.9 + - + +
65D ASP* 5.3 5.0 - - - +
99D ILE* 4.4 19.9 + - + +
101D GLU* 4.8 18.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 46 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38D GLU* 3.5 4.7 - - - +
39D ILE* 2.9 54.1 + - + +
41D THR* 4.5 10.8 - - + -
44D GLY 4.1 0.4 + - - -
45D LYS* 1.3 73.9 - - - +
47D VAL* 1.3 74.4 + - - +
48D LEU* 4.5 9.0 - - + -
63D ALA* 5.1 0.9 - - + -
64D MET 4.3 1.8 - - - +
65D ASP* 3.4 46.4 - - + +
66D GLY 4.2 14.6 - - - +
67D THR* 4.4 4.3 - - - -
70D LEU* 4.0 31.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 47 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36D ALA* 4.5 12.3 - - + -
37D LEU 3.4 8.3 - - - +
38D GLU* 5.2 4.5 - - + -
45D LYS* 3.8 27.1 - - + +
46D LEU* 1.3 81.7 - - - +
48D LEU* 1.3 75.8 + - - +
64D MET* 3.1 48.0 + - + +
65D ASP* 5.4 1.2 - - - +
83D ILE* 4.6 11.9 - - + -
99D ILE* 3.7 30.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 48 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13D VAL* 5.5 0.2 - - + -
21D VAL* 3.8 39.0 - - + -
23D VAL* 4.8 6.1 - - + -
36D ALA* 3.3 7.3 - - - +
37D LEU* 2.8 46.1 + - + +
39D ILE* 4.7 11.4 - - + -
46D LEU* 4.5 10.3 - - + -
47D VAL* 1.3 87.6 - - - +
49D GLU* 1.3 61.7 + - - +
50D VAL 4.3 0.2 - - - -
61D THR* 3.9 13.9 - - + +
62D ILE 3.4 15.9 - - - +
63D ALA* 3.7 13.9 - - + -
64D MET* 4.5 1.3 - - - -
70D LEU* 6.2 0.9 - - + -
76D VAL* 4.5 20.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 49 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34D LEU* 3.3 22.5 - - - +
35D ASN 4.2 3.4 - - - +
36D ALA* 4.6 0.4 - - - +
48D LEU* 1.3 74.6 - - - +
50D VAL* 1.3 71.8 + - - +
51D ALA* 3.4 0.9 + - - +
61D THR* 3.3 4.8 - - - -
62D ILE* 3.0 38.6 + - + +
64D MET* 3.3 18.6 - - + +
83D ILE* 4.3 14.4 - - + -
118D HIS* 2.9 30.8 + - - -
231D ARG* 2.5 43.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 50 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31D PRO* 4.1 19.7 - - + +
32D ALA 3.5 21.5 - - - +
33D ILE* 3.7 21.9 - - + +
34D LEU* 3.1 24.3 + - - +
35D ASN 3.3 24.0 + - - +
37D LEU* 4.1 9.4 - - + -
49D GLU* 1.3 76.1 - - - +
51D ALA* 1.3 61.5 + - - +
53D HIS* 4.4 2.2 - - - +
59D VAL* 3.6 29.4 - - + -
61D THR* 3.7 11.9 - - + -
231D ARG* 5.9 0.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 51 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37A GLY* 4.4 5.4 - - - -
38A ASP* 4.6 4.7 + - - +
81A ASP* 5.0 0.5 - - - +
33D ILE* 3.6 22.8 - - - +
34D LEU* 5.8 1.1 - - - -
49D GLU 3.4 1.0 + - - +
50D VAL* 1.3 75.2 - - - +
52D GLN* 1.3 65.5 + - + +
60D ARG 3.1 13.4 + - - +
62D ILE* 4.1 23.3 - - + -
231D ARG* 6.0 1.3 - - - +
272D LEU* 3.9 26.0 - - + -
274D ARG* 5.5 2.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 52 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36A VAL 4.0 5.8 - - - +
37A GLY* 4.0 13.7 - - - -
38A ASP* 3.0 31.3 + - - +
33D ILE* 4.4 0.9 - - - -
51D ALA* 1.3 86.6 - - + +
53D HIS* 1.3 68.8 + - - +
54D LEU* 3.9 18.3 - - + +
59D VAL* 3.3 10.0 - - - +
60D ARG* 2.9 41.0 + - + +
272D LEU* 3.4 42.8 + - + +
273D GLY 5.1 1.6 + - - -
274D ARG* 4.3 0.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 53 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35A ALA* 3.3 14.1 - - - +
36A VAL* 2.8 37.7 + - + +
84A VAL 4.1 3.6 - - - -
85A LYS* 3.9 22.2 - - + -
86A GLU* 3.5 29.8 + - + +
30D LEU* 4.9 7.6 - - + -
31D PRO 3.0 27.4 + - - -
32D ALA* 4.3 2.9 - - - -
33D ILE* 3.5 24.9 - - + +
50D VAL* 4.4 0.6 - - - +
52D GLN* 1.3 72.1 - - - +
54D LEU* 1.3 60.8 + - - +
55D GLY 3.1 10.7 + - - +
58D THR 3.8 4.5 - - - +
59D VAL* 3.6 23.2 - - + +
----------------------------------------------------------
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