Contacts of the strand formed by residues 11 - 17 (chain X) in PDB entry 3SDI
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 SER 11 (chain X).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7X ARG* 3.5 2.8 - - - -
8X VAL* 2.9 36.3 + - - +
10X ASP* 1.3 82.6 - - - +
12X VAL* 1.3 60.5 + - - +
13X ILE* 4.4 2.1 - - - +
108X PRO* 3.5 13.9 - - - +
148X THR* 2.7 27.1 + - - +
177X ILE* 3.5 21.7 - - - +
178X VAL 3.2 14.6 - - - -
179X ASP* 3.8 7.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 12 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6X ILE 3.5 10.1 - - - +
7X ARG* 3.7 9.9 - - + -
11X SER* 1.3 73.9 - - - +
13X ILE* 1.3 70.5 + - - +
14X LEU* 4.5 2.9 - - + -
102X GLY* 3.9 15.0 - - - -
103X GLY 4.0 5.4 - - - +
108X PRO* 3.5 23.3 - - + -
109X GLU 3.5 23.8 - - - +
110X LEU* 3.8 30.5 - - + -
176X LYS 3.7 0.9 - - - +
177X ILE* 3.5 2.4 - - - +
178X VAL* 2.9 40.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 13 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5X GLY* 3.3 4.7 - - - -
6X ILE* 2.8 48.4 + - + +
8X VAL* 4.5 10.8 - - + -
11X SER* 4.4 9.2 - - - +
12X VAL* 1.3 80.6 - - - +
14X LEU* 1.3 61.9 + - - +
148X THR* 4.1 8.5 - - + +
151X GLY* 3.7 38.1 - - - +
152X LEU* 3.8 17.9 - - + +
155X LEU* 3.9 10.8 - - + +
175X VAL* 3.3 33.2 - - + -
176X LYS 3.4 6.5 - - - +
177X ILE* 4.5 6.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 14 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4X LEU 3.6 3.8 - - - +
5X GLY* 3.8 15.9 - - - -
12X VAL* 4.2 6.0 - - + -
13X ILE* 1.3 84.8 - - - +
15X ALA* 1.3 60.0 + - - +
16X SER* 4.7 2.9 - - - +
34X THR* 4.4 2.0 - - - +
42X LEU* 4.1 39.5 - - + +
44X SER* 3.7 41.5 - - - +
100X LEU* 4.4 6.1 - - + +
102X GLY* 4.5 5.2 - - - +
110X LEU* 3.9 18.6 - - + -
174X ILE 3.4 2.0 - - - +
175X VAL* 3.2 5.5 - - - +
176X LYS* 2.9 38.3 + - + +
178X VAL* 5.5 2.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 15 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2X ILE* 3.7 1.0 - - - +
3X ILE* 3.4 0.5 - - - -
4X LEU* 2.8 51.9 + - + +
13X ILE 4.3 0.4 - - - -
14X LEU* 1.3 75.3 - - - +
16X SER* 1.3 64.1 + - - +
155X LEU* 3.5 28.5 - - + +
159X VAL* 5.3 0.9 - - + -
173X VAL* 4.1 16.2 - - + -
174X ILE 3.2 7.2 - - - +
175X VAL* 4.0 6.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 16 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2X ILE 3.2 7.9 - - - -
3X ILE* 4.0 3.5 - - - +
14X LEU* 4.7 2.9 - - - +
15X ALA* 1.3 81.0 + - - +
17X SER* 1.3 64.6 + - - +
31X ASP 5.1 0.7 - - - +
32X ASP* 5.9 0.7 - - - -
33X LYS* 4.1 29.2 + - - -
34X THR* 5.2 3.5 - - - -
44X SER* 3.8 22.5 - - - -
173X VAL* 3.1 6.4 - - - +
174X ILE* 2.8 39.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 17 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1X ASP* 3.5 15.2 + - - +
2X ILE* 2.8 36.1 + - - -
16X SER* 1.3 75.0 - - - +
18X LYS* 1.3 60.9 + - - +
19X ALA* 4.5 3.5 + - - +
31X ASP 3.7 4.3 - - - +
33X LYS* 3.2 29.4 + - - +
170X PHE* 3.6 33.0 - - - +
172X GLY 3.4 7.2 - - - -
173X VAL* 4.0 3.0 - - - +
----------------------------------------------------------
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