Contacts of the strand formed by residues 51 - 61 (chain A) 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 A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43A ILE 4.2 4.0 - - - +
44A ASP* 3.8 32.8 - - + +
50A LYS* 1.3 77.6 - - - +
52A LEU* 1.3 59.7 + - - +
233A THR* 3.4 5.7 - - - +
234A MET* 2.8 37.1 + - + +
236A ARG* 3.7 31.5 + - + +
241A GLN* 3.1 28.5 + - - +
286A TRP* 2.9 52.2 + - + +
287A GLU* 4.1 9.3 - - - +
289A GLU* 6.0 0.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 52 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14A ILE* 5.3 8.3 - - + -
42A PHE* 3.5 5.0 - - - +
43A ILE* 2.8 54.1 + - + +
48A HIS* 4.6 18.4 - - + +
50A LYS 4.6 2.7 - - - +
51A LYS* 1.3 76.1 - - - +
53A LEU* 1.3 74.3 + - - +
54A VAL* 3.6 23.6 - - + -
99A SER* 5.6 0.2 - - - +
231A VAL* 3.2 35.0 - - + -
232A ILE 3.6 2.7 - - - +
233A THR* 3.6 21.3 - - + -
286A TRP* 3.8 5.6 - - - -
24B ASP* 5.8 1.1 - - - +
7G ILE* 4.2 13.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 53 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40A TYR* 4.0 9.4 - - + -
41A SER 3.4 24.0 - - - +
42A PHE* 3.7 28.9 - - + -
52A LEU* 1.3 73.3 - - - +
54A VAL* 1.3 62.8 + - - +
55A ILE* 3.9 20.5 + - + -
230A THR 3.6 1.4 - - - +
231A VAL* 3.3 3.1 - - - -
232A ILE* 2.8 41.2 + - + +
284A ILE* 3.5 46.2 - - + -
286A TRP* 3.4 22.4 - - + -
291A MET* 4.3 3.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 54 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39A PHE 3.7 1.0 - - - +
40A TYR* 3.2 6.6 - - - +
41A SER* 2.9 44.3 + - - +
43A ILE* 4.2 6.3 - - + -
52A LEU* 3.6 14.1 - - + -
53A LEU* 1.3 70.6 - - - +
55A ILE* 1.3 63.3 + - - +
56A ARG* 3.7 30.9 + - + +
229A ALA* 4.6 4.9 - - + -
230A THR 3.5 8.1 - - - +
231A VAL* 4.5 2.5 - - + +
5G ILE* 4.0 19.3 - - + -
7G ILE* 3.5 30.7 - - + -
12G THR* 4.6 3.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 55 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38A VAL* 3.9 23.1 - - + -
39A PHE 3.9 1.8 - - - -
40A TYR* 4.6 1.1 - - + +
53A LEU* 3.9 24.0 - - + +
54A VAL* 1.3 73.7 - - - +
56A ARG* 1.3 64.0 + - - +
57A THR* 3.8 10.9 + - + +
88A LEU* 3.9 21.5 - - + -
228A PHE 3.7 0.9 - - - +
229A ALA* 3.5 1.0 - - - -
230A THR* 2.7 41.7 + - - +
232A ILE* 3.7 27.6 - - + -
245A ILE* 4.0 13.7 - - + -
247A VAL* 5.5 2.5 - - + -
284A ILE* 4.4 0.9 - - + -
291A MET* 4.0 24.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 56 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37A LYS 3.6 0.7 - - - +
38A VAL* 3.4 6.4 - - - +
39A PHE* 2.8 53.6 + - + +
41A SER* 4.4 1.6 + - - -
54A VAL* 3.7 23.2 + - + +
55A ILE* 1.3 74.0 - - - +
57A THR* 1.3 61.3 + - - +
58A LYS* 3.7 14.3 + - + +
227A ASP* 5.1 7.0 - - - +
228A PHE 3.2 10.1 - - - +
229A ALA* 4.2 15.2 - - + +
6F ASN* 3.7 22.4 - - - +
1G ALA 5.3 1.4 - - - -
2G ASP* 2.8 31.5 + - - +
5G ILE* 4.7 8.1 - - - +
12G THR* 2.8 33.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 57 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37A LYS 3.7 4.3 - - - -
38A VAL* 4.8 5.6 - - + -
55A ILE* 3.8 8.5 + - + +
56A ARG* 1.3 72.1 - - - +
58A LYS* 1.3 60.6 + - - +
86A VAL* 3.6 23.5 - - + +
88A LEU* 4.1 27.9 - - + +
167A TRP* 4.7 0.2 - - - -
226A PRO* 3.4 9.2 - - - +
228A PHE* 2.9 42.5 + - - +
230A THR* 5.6 0.2 + - - -
247A VAL* 4.2 16.4 - - + -
249A TYR* 3.5 13.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 58 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37A LYS* 2.9 36.8 + - - -
39A PHE* 4.9 0.9 - - + -
56A ARG* 4.3 20.6 - - + +
57A THR* 1.3 78.6 - - - +
59A GLY* 1.3 68.1 + - - +
226A PRO* 3.1 17.3 - - - +
227A ASP* 3.9 22.2 + - - +
249A TYR* 2.6 30.3 + - - -
4F ASP 2.9 17.2 + - - -
6F ASN* 2.9 25.5 + - - +
100G ASP* 2.7 31.6 + - - +
104G ARG* 3.7 14.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 59 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35A HIS* 3.3 18.8 - - - -
37A LYS* 4.2 7.9 - - - +
58A LYS* 1.3 81.8 - - - +
60A THR* 1.3 71.5 + - - +
225A SER* 3.2 19.9 - - - -
226A PRO* 3.3 3.0 - - - +
99G SER 5.3 0.8 + - - -
100G ASP* 5.6 1.8 + - - -
101G TYR* 3.1 16.4 - - - -
104G ARG* 5.4 0.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 60 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34A MET* 3.8 1.0 - - - -
35A HIS* 2.9 38.0 + - - +
58A LYS 4.0 0.2 + - - -
59A GLY* 1.3 68.8 - - - +
61A ILE* 1.3 69.6 + - - +
62A ALA 3.9 1.4 + - - -
222A SER 4.5 5.9 + - - -
223A GLY 4.7 0.9 - - - -
224A PHE 3.2 12.4 + - - -
225A SER* 3.0 28.9 - - - +
226A PRO* 3.9 2.7 - - - -
249A TYR* 5.1 0.4 - - - -
101G TYR* 2.6 39.8 + - + +
157G LEU* 4.2 2.8 - - + +
159G SER* 4.8 0.2 - - - -
160G PRO* 3.4 27.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 61 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33A GLY 4.0 2.7 - - - -
34A MET* 3.9 21.1 - - + -
60A THR* 1.3 75.5 - - - +
62A ALA* 1.3 78.5 + - - +
84A PHE* 3.7 31.7 - - + -
85A LYS 4.0 14.4 - - - +
86A VAL* 4.7 0.7 - - + -
223A GLY* 3.2 0.2 - - - -
224A PHE* 2.8 32.1 + - + +
226A PRO* 4.4 12.8 - - + -
249A TYR* 3.8 29.6 - - + -
250A GLU 3.8 17.9 - - - +
251A ARG* 3.6 17.5 - - + +
----------------------------------------------------------
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