Contacts of the strand formed by residues 21 - 30 (chain B) in PDB entry 4LML
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 ILE 21 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20B GLY* 1.3 79.1 - - - +
22B TYR* 1.3 62.0 + - - +
23B LEU* 4.1 6.6 + - + -
40B ALA* 3.9 17.9 - - + -
41B PHE 3.3 8.5 - - - +
42B LEU* 3.9 14.1 - - + -
77B PHE* 4.4 12.8 - - + -
105B PHE* 4.4 6.5 - - + -
127B ILE* 4.8 7.2 - - + -
129B LEU* 4.2 17.3 - - + -
146B GLU 2.9 18.5 + - - +
147B LYS 3.5 5.4 - - - +
149B GLY* 3.5 12.5 + - - -
164B PHE* 4.0 17.0 - - + -
185B TYR* 3.6 47.0 - - + -
176E GLU* 4.8 0.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 22 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21B ILE* 1.3 72.8 - - - +
23B LEU* 1.3 75.3 + - - +
24B ILE* 3.3 16.9 + - + +
40B ALA* 3.3 3.2 - - - -
41B PHE* 2.9 48.4 + + + +
146B GLU 4.9 0.4 - - - +
148B VAL* 6.1 0.9 - - + -
149B GLY* 3.2 20.4 - - - -
150B LYS 2.9 29.6 + - - -
151B ASN* 3.9 16.0 + - + -
173E PHE* 5.8 5.5 - - - -
175E LEU* 3.5 40.7 - - + +
176E GLU* 3.4 22.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 23 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21B ILE* 4.0 10.1 - - + -
22B TYR* 1.3 75.6 - - - +
24B ILE* 1.3 59.0 + - - +
25B GLU 5.3 0.4 - - - +
26B CYS* 4.4 11.0 - - - -
38B VAL* 3.6 27.8 - - + -
39B ASN 4.4 0.2 - - - -
40B ALA* 3.7 3.1 - - + -
127B ILE* 5.2 3.6 - - + -
149B GLY 3.4 11.7 + - - +
150B LYS* 3.2 13.9 - - + -
151B ASN 3.1 24.7 + - - -
154B VAL* 4.4 9.0 - - + -
161B ILE* 6.1 0.4 - - + -
164B PHE* 3.7 55.9 - - + -
187B LEU* 4.2 22.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 24 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22B TYR* 3.7 22.4 - - + +
23B LEU* 1.3 74.7 - - - +
25B GLU* 1.3 77.5 - - + +
39B ASN* 2.9 13.2 + - - +
40B ALA* 3.7 22.4 - - - -
41B PHE* 3.8 22.0 - - + +
104B ARG* 3.6 43.7 - - + +
151B ASN* 3.5 17.8 - - - +
154B VAL* 3.3 15.6 - - - +
76E ARG* 5.4 0.7 - - - +
78E VAL* 4.2 17.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 25 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23B LEU* 5.8 0.4 - - - -
24B ILE* 1.3 95.7 - - + +
26B CYS* 1.3 63.8 + - - +
27B TYR* 4.2 12.4 - - + -
38B VAL* 3.9 2.3 - - - +
39B ASN* 3.0 40.4 + - + +
151B ASN* 4.6 8.0 + - - -
153B ASP* 4.5 11.8 - - - +
154B VAL* 4.5 11.1 - - - -
155B PHE* 4.5 7.6 + - - +
78E VAL* 4.1 6.1 - - - +
79E ASN* 3.7 38.0 + - - +
80E VAL 4.5 9.0 - - - +
110E LEU* 4.6 13.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 26 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23B LEU* 4.4 11.9 - - - -
25B GLU* 1.3 78.1 + - - +
27B TYR* 1.3 65.8 + - - +
36B PHE* 4.7 9.2 - - - -
37B LYS 3.7 11.7 - - - -
38B VAL* 4.2 17.3 - - - -
154B VAL* 4.6 8.2 - - + +
155B PHE* 3.7 15.9 - - - +
156B LEU* 3.1 40.9 + - + +
161B ILE* 5.3 1.8 - - + -
187B LEU* 4.2 24.2 - - + -
110E LEU* 4.7 2.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 27 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25B GLU* 4.2 12.1 - - + -
26B CYS* 1.3 83.4 - - - +
28B SER* 1.3 78.6 - - - +
29B LEU 3.4 3.1 + - - -
37B LYS* 3.1 65.4 + - + +
38B VAL 5.1 2.4 + - - -
39B ASN* 4.6 9.1 - - + +
106B SER* 5.4 1.7 - - - -
155B PHE* 5.9 0.7 - - + -
156B LEU* 4.1 13.3 - - - +
157B THR* 5.4 4.3 - - + +
33E ALA 5.8 2.2 - - - +
81E GLU* 3.0 68.2 + - + +
82E ASN* 4.5 5.2 + - - -
110E LEU* 3.4 30.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 28 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27B TYR* 1.3 95.2 - - - +
29B LEU* 1.3 65.1 + - - +
30B ASP* 3.2 6.8 + - - +
35B THR 3.6 1.2 - - - +
36B PHE* 3.4 13.2 - - - -
37B LYS* 3.7 25.8 + - - +
108B ARG* 5.5 1.7 + - - -
156B LEU* 4.7 0.6 - - - +
157B THR* 5.5 4.2 + - - +
33E ALA* 6.0 1.6 - - - +
81E GLU* 4.6 3.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 29 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27B TYR 3.4 2.4 - - - -
28B SER* 1.3 74.4 - - - +
30B ASP* 1.3 60.5 + - - +
31B ASP* 3.7 25.1 + - - +
35B THR 4.8 1.1 - - - +
36B PHE* 3.7 14.4 - - + -
113B LEU* 4.6 14.6 - - + -
125B LEU* 3.9 18.4 - - + -
156B LEU* 3.5 22.7 - - + +
157B THR 6.0 0.4 - - - +
159B TRP* 3.6 34.7 + - + +
189B ILE* 3.5 32.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 30 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28B SER 3.2 4.6 + - - +
29B LEU* 1.3 74.3 - - - +
31B ASP* 1.3 58.5 + - - +
32B LYS* 3.1 19.3 + - - +
33B ALA* 3.3 22.8 + - + +
34B GLU* 2.7 34.8 + - - -
35B THR* 2.7 20.5 + - - +
108B ARG* 4.7 6.0 + - - +
113B LEU* 4.2 1.6 - - - +
----------------------------------------------------------
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