Contacts of the strand formed by residues 34 - 43 (chain D) in PDB entry 3M4D
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 MET 34 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27D THR 3.7 0.5 - - - +
28D TYR* 3.3 6.5 - - - -
29D ASP* 2.8 39.6 + - + -
32D ASN* 3.4 25.1 - - + +
33D GLY* 1.3 77.7 - - - +
35D HIS* 1.3 61.1 + - - +
36D LYS* 3.6 14.0 + - + +
60D THR 3.8 4.7 - - - +
61D ILE* 3.9 25.1 - - + -
249D TYR* 3.6 35.0 - - + +
250D GLU* 3.8 3.6 - - - -
251D ARG* 3.7 20.2 - - + +
276D ASP 3.6 17.9 - - - +
278D SER* 3.6 18.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 35 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98C ILE 3.0 26.5 + - - -
99C SER 3.7 14.8 - - - -
101C TYR* 2.7 41.2 + + - -
160C PRO 3.5 20.8 + - - +
161C THR 3.5 24.3 + - - -
162C ASP* 3.7 6.5 - - + -
26D VAL* 3.5 17.3 - - + +
27D THR 3.9 1.6 - - - -
28D TYR* 3.6 7.9 - + + -
33D GLY 4.3 0.2 - - - -
34D MET* 1.3 70.1 - - - +
36D LYS* 1.3 60.0 + - - +
37D LYS* 4.6 3.4 - - + -
59D GLY* 3.2 8.6 - - - -
60D THR* 2.8 42.5 + - + +
249D TYR* 4.2 3.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 36 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25D LEU 3.7 1.1 - - - +
26D VAL* 3.4 5.0 - - - +
27D THR* 2.8 60.3 + - - +
29D ASP* 4.8 4.7 - - - -
34D MET* 3.8 11.0 - - + +
35D HIS* 1.3 76.2 - - - +
37D LYS* 1.3 61.0 + - - +
38D VAL* 6.5 0.2 - - + -
247D VAL* 4.9 1.4 + - + -
249D TYR* 3.8 48.0 - - + -
278D SER* 2.8 39.3 + - - +
279D SER 4.0 1.0 - - - -
280D GLU* 3.3 38.4 + - - +
282D TYR* 5.0 9.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 37 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6B ASN* 4.9 2.6 + - - -
99C SER* 2.8 36.5 + - - +
100C ASP* 3.9 13.4 + - - +
231C VAL* 5.9 0.6 - - - +
24D ASP* 2.7 29.5 + - - +
25D LEU 3.3 3.6 - - - +
26D VAL* 3.5 24.9 - - + -
35D HIS* 4.1 3.3 + - + -
36D LYS* 1.3 75.0 - - - +
38D VAL* 1.3 76.0 + - - +
39D PHE* 3.7 7.6 - - - +
56D ARG 3.6 0.5 - - - +
57D THR* 3.7 1.4 - - - -
58D LYS* 2.9 63.6 + - + -
59D GLY* 4.1 12.8 - - - +
249D TYR* 3.7 5.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 38 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23D GLY 3.8 0.7 - - - +
24D ASP* 3.4 3.8 - - - -
25D LEU* 2.9 42.9 + - + +
36D LYS* 6.5 0.2 - - + -
37D LYS* 1.3 82.8 - - - +
39D PHE* 1.3 67.1 + - - +
40D TYR* 4.2 4.9 + - + +
55D ILE* 3.9 24.2 - - + -
56D ARG 3.4 2.9 - - - -
57D THR* 4.6 17.3 - - + -
247D VAL* 5.2 3.6 - - + -
249D TYR* 5.5 1.6 - - + +
282D TYR* 3.5 34.3 - - + +
291D MET* 4.2 20.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 39 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6B ASN* 3.8 38.8 - - + +
12C THR 3.3 26.7 - - - -
14C ILE* 3.1 37.0 - - + -
48C HIS* 3.5 7.4 - + - -
22D THR* 4.1 7.9 - - - -
23D GLY 3.3 9.4 - - - -
24D ASP* 3.6 20.2 - - - +
37D LYS* 3.7 12.5 - - - +
38D VAL* 1.3 74.2 - - - +
40D TYR* 1.3 59.6 + - - +
41D SER* 3.5 14.8 - - - -
54D VAL 3.8 1.4 - - - +
56D ARG* 2.9 52.8 + - + +
58D LYS* 4.9 0.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 40 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49C ASN* 3.8 22.1 + - - +
21D LYS* 4.3 1.6 - - + -
22D THR* 3.2 9.3 + - - -
23D GLY* 2.9 59.4 + - - +
24D ASP 4.3 0.2 - - - -
25D LEU* 4.1 11.7 - - + -
38D VAL* 4.4 6.3 - - + -
39D PHE* 1.3 76.5 - - - +
41D SER* 1.3 72.9 + - - +
42D PHE* 3.6 35.7 - + - -
53D LEU* 3.9 4.0 - - + -
54D VAL 3.2 9.0 - - - +
55D ILE* 4.7 1.6 - - - -
289D GLU 4.5 2.3 + - - -
290D GLU* 4.0 7.8 - - - +
291D MET* 3.4 62.6 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 41 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12C THR* 3.3 40.8 - - - +
20D VAL* 4.1 5.2 - - - -
21D LYS 3.4 6.3 - - - -
22D THR* 3.6 10.4 - - - +
39D PHE* 3.5 11.8 - - - -
40D TYR* 1.3 81.5 + - - +
42D PHE* 1.3 60.4 - - - +
43D ILE* 3.7 3.9 + - - +
53D LEU* 3.4 5.7 - - - -
54D VAL* 2.9 36.3 + - - +
56D ARG* 4.2 1.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 42 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19D THR 4.4 0.9 - - - +
20D VAL* 3.4 9.7 - - - +
21D LYS* 2.8 32.8 + - + +
40D TYR* 3.6 29.8 - + - -
41D SER* 1.3 71.4 - - - +
43D ILE* 1.3 59.3 + - - +
44D ASP 4.0 1.5 + - - -
52D LEU 3.5 2.7 - - - -
53D LEU* 4.0 14.1 - - + -
284D ILE* 3.7 28.5 - - + -
285D ASP 3.8 9.0 - - - -
286D TRP* 3.9 25.6 - + - -
289D GLU* 3.3 57.0 - - + +
290D GLU 3.3 24.5 - - - -
291D MET* 4.0 1.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 43 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7C ILE* 3.6 34.5 - - + -
11C THR* 4.0 17.3 - - + -
12C THR* 4.1 9.9 - - + -
14D ILE* 4.1 14.3 - - + +
15D GLY* 4.0 25.1 - - - -
18D THR* 4.5 8.3 - - + -
20D VAL* 4.2 17.3 - - + -
41D SER 4.2 6.3 - - - +
42D PHE* 1.3 77.9 - - - +
44D ASP* 1.3 58.0 + - - +
45D ASP* 3.5 8.0 + - + +
50D LYS 4.6 0.7 - - - +
51D LYS* 3.9 1.0 - - - -
52D LEU* 2.9 42.9 + - + +
54D VAL* 4.3 6.1 - - + -
----------------------------------------------------------
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