Contacts of the strand formed by residues 51 - 61 (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 LYS 51 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43D ILE 4.0 6.3 - - - +
44D ASP* 4.0 20.9 - - + +
50D LYS* 1.3 75.0 - - - +
52D LEU* 1.3 58.3 - - - +
233D THR* 3.4 4.7 - - - -
234D MET* 2.9 38.5 + - + +
236D ARG* 3.5 43.1 + - + +
241D GLN* 2.9 32.2 + - - +
286D TRP* 3.3 47.9 + - + +
287D GLU* 4.2 9.1 - - - +
289D GLU* 6.0 1.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 52 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5C ILE 5.8 1.1 - - - +
7C ILE* 4.7 17.3 - - + -
14D ILE* 3.8 36.1 - - + -
41D SER 4.4 0.2 - - - -
42D PHE* 3.5 4.5 - - - +
43D ILE* 2.9 47.9 + - + +
48D HIS* 3.9 14.6 - - + +
50D LYS 5.1 0.4 - - - -
51D LYS* 1.3 77.0 - - - +
53D LEU* 1.3 61.8 + - - +
54D VAL* 4.3 0.9 - - + -
231D VAL* 3.9 18.4 - - + -
232D ILE 3.4 2.7 - - - -
233D THR* 3.2 35.7 - - + -
286D TRP* 3.7 6.2 - - - -
24E ASP* 3.9 11.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 53 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40D TYR* 3.9 13.5 - - + -
41D SER 3.4 28.9 - - - +
42D PHE* 4.0 18.4 - - + -
52D LEU* 1.3 73.8 - - - +
54D VAL* 1.3 63.3 + - - +
55D ILE* 3.8 21.5 + - + -
230D THR 3.6 1.0 - - - +
231D VAL* 3.3 3.5 - - - -
232D ILE* 2.8 36.5 + - + +
284D ILE* 3.4 46.7 - - + -
286D TRP* 3.4 20.9 - - + -
291D MET* 4.2 4.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 54 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5C ILE* 4.0 16.8 - - + -
7C ILE* 3.4 32.3 - - + -
12C THR* 4.6 2.2 - - + -
39D PHE 3.8 1.0 - - - +
40D TYR* 3.2 6.1 - - - +
41D SER* 2.9 38.6 + - - +
43D ILE* 4.3 11.7 - - + -
52D LEU* 5.5 1.3 - - + -
53D LEU* 1.3 76.3 - - - +
55D ILE* 1.3 63.7 + - - +
56D ARG* 3.7 37.9 - - + +
229D ALA* 4.6 4.5 - - + -
230D THR 3.5 7.6 - - - +
231D VAL* 4.7 8.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 55 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38D VAL* 3.9 23.3 - - + -
39D PHE 3.9 2.0 - - - -
40D TYR* 4.6 0.9 - - - +
53D LEU* 3.8 20.0 - - + -
54D VAL* 1.3 75.0 - - - +
56D ARG* 1.3 62.1 + - - +
57D THR* 3.9 9.7 + - + -
88D LEU* 4.0 18.4 - - + -
228D PHE 3.8 0.5 - - - +
229D ALA* 3.4 2.1 - - - -
230D THR* 2.8 45.2 + - - +
232D ILE* 3.4 32.1 - - + -
245D ILE* 4.0 13.0 - - + -
247D VAL* 5.8 0.4 - - + -
284D ILE* 4.5 0.7 - - + -
291D MET* 3.7 26.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 56 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6B ASN* 3.6 23.5 - - - +
1C ALA 5.8 0.6 - - - -
2C ASP* 2.6 30.7 + - - +
5C ILE* 4.7 6.7 - - - +
12C THR* 3.0 31.3 + - - +
37D LYS 3.6 0.2 - - - +
38D VAL* 3.4 5.7 - - - -
39D PHE* 2.9 54.8 + - + +
41D SER* 4.2 1.8 + - - -
54D VAL* 3.7 22.9 + - + +
55D ILE* 1.3 76.3 - - - +
57D THR* 1.3 62.1 + - - +
58D LYS* 3.6 13.8 + - + +
227D ASP* 5.2 6.5 - - - +
228D PHE 3.2 7.2 - - - +
229D ALA* 4.2 18.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 57 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37D LYS 3.7 4.5 - - - -
38D VAL* 4.6 7.0 - - + -
55D ILE* 3.9 9.1 + - + +
56D ARG* 1.3 70.6 - - - +
58D LYS* 1.3 61.2 + - - +
86D VAL* 3.6 24.2 - - + +
88D LEU* 4.2 28.3 - - + +
167D TRP* 4.8 0.2 - - - -
226D PRO* 3.4 9.1 - - - +
228D PHE* 2.9 43.6 + - - +
230D THR* 5.5 0.3 - - - +
247D VAL* 4.3 11.7 - - + -
249D TYR* 3.5 14.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 58 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4B ASP 3.0 18.0 + - - -
6B ASN* 2.9 27.6 + - - +
100C ASP* 2.7 30.7 + - - +
104C ARG* 3.7 15.3 - - - +
37D LYS* 2.9 34.6 + - - -
39D PHE* 4.9 1.1 - - + -
56D ARG* 4.3 19.3 - - + +
57D THR* 1.3 77.7 - - - +
59D GLY* 1.3 68.3 + - - +
226D PRO* 3.1 18.9 - - - +
227D ASP* 4.0 23.6 + - - +
249D TYR* 2.6 30.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 59 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99C SER 5.4 1.3 + - - -
100C ASP* 5.6 1.8 + - - -
101C TYR* 3.1 21.2 + - - -
104C ARG* 5.3 0.3 + - - -
35D HIS* 3.2 16.8 - - - -
37D LYS* 4.1 10.8 - - - +
58D LYS* 1.3 82.4 - - - +
60D THR* 1.3 58.4 + - - -
225D SER* 3.2 26.3 - - - -
226D PRO* 3.3 2.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 60 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101C TYR* 3.1 7.2 - - - +
157C LEU* 5.1 2.1 - - - +
159C SER* 5.2 0.4 - - - -
160C PRO* 3.0 48.4 - - + +
33D GLY 4.3 0.2 - - - +
34D MET* 3.8 0.9 - - - -
35D HIS* 2.8 39.0 + - + -
58D LYS 4.0 0.2 + - - -
59D GLY* 1.3 74.8 - - - -
61D ILE* 1.3 71.6 + - - +
62D ALA* 3.8 2.2 + - - +
222D SER 4.4 6.1 + - - -
223D GLY 4.4 1.2 - - - -
224D PHE 3.3 15.3 + - - -
225D SER* 3.6 13.5 + - - +
226D PRO* 4.0 1.5 - - - +
249D TYR* 5.0 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 61 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33D GLY 4.1 2.9 - - - -
34D MET* 3.9 20.4 - - + -
60D THR* 1.3 74.5 - - - +
62D ALA* 1.3 67.9 + - - +
84D PHE* 3.7 29.9 - - + -
85D LYS 3.9 11.9 - - - +
86D VAL* 4.5 0.9 - - + -
223D GLY* 3.2 0.2 - - - -
224D PHE* 2.8 32.8 + - + +
226D PRO* 4.4 12.8 - - + -
249D TYR* 3.7 36.8 - - + -
250D GLU 3.9 16.8 - - - +
251D ARG* 3.5 26.5 - - + +
----------------------------------------------------------
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