Contacts of the strand formed by residues 2 - 7 (chain M) 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 VAL 2 (chain M).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1M SER* 1.3 76.3 - - - +
3M ILE* 1.3 65.2 + - - +
13M ILE* 3.8 32.1 - - + -
14M ALA 3.5 8.1 - - - +
15M ALA* 4.2 7.6 - - + -
32M ARG* 3.7 7.9 - - - +
33M LEU* 4.8 0.9 - - + -
43M GLY* 3.7 12.6 - - - +
44M ILE 3.7 35.9 - - - +
45M SER* 3.9 4.7 - - - +
106M ILE* 3.7 11.3 - - + +
134M ALA* 3.2 3.6 - - - -
135M THR* 2.8 38.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 3 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1M SER* 4.0 3.1 - - - -
2M VAL* 1.3 79.9 - - - +
4M SER* 1.3 61.5 + - - +
13M ILE* 3.3 3.3 - - - +
14M ALA* 2.7 37.3 + - + +
133M LEU 3.6 5.2 - - - -
134M ALA* 3.9 12.6 - - + -
138M GLY* 4.0 5.2 - - - -
142M ALA* 3.8 22.0 - - + -
146M LEU* 4.3 4.0 - - + -
168M ILE* 3.8 32.2 - - + +
171M ALA* 3.6 31.6 - - + -
172M MET* 4.0 21.1 - - - -
175M LEU* 3.9 17.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 4 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3M ILE* 1.3 78.4 - - - +
5M MET* 1.3 64.1 + - - +
12M ILE 3.1 14.6 - - - -
13M ILE* 3.9 14.6 - - - -
106M ILE* 3.8 6.7 - - - +
118M LEU* 3.6 19.6 - - - +
132M THR* 3.5 3.5 - - - -
133M LEU* 2.9 54.4 + - - +
146M LEU* 3.8 4.5 - - - +
168M ILE* 4.0 8.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 5 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4M SER* 1.3 76.8 - - - +
6M LYS* 1.3 67.5 + - - +
7M TYR 4.2 0.2 + - - -
11M VAL* 3.5 3.5 - - - +
12M ILE* 3.0 31.7 + - + +
118M LEU* 4.1 8.3 - - - -
131M PRO 3.4 13.7 - - - +
132M THR* 3.9 8.5 - - + +
146M LEU* 3.9 24.9 - - + +
149M VAL* 4.1 18.6 - - + -
150M VAL* 3.6 35.7 - - + -
159M THR* 4.5 1.1 - - + -
164M ALA* 3.8 39.3 - - + +
167M ALA* 4.3 2.9 - - - -
168M ILE* 4.2 10.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 6 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5M MET* 1.3 90.7 - - - +
7M TYR* 1.3 64.2 + - - +
10M GLY 3.4 13.5 - - - +
11M VAL* 3.8 7.9 - - + -
116M GLN* 3.9 31.6 + - + +
117M PHE 4.9 0.2 - - - -
118M LEU* 3.7 30.7 - - - +
129M SER* 4.7 7.5 + - - -
130M SER 4.2 13.2 + - - -
131M PRO* 3.0 14.7 + - + +
150M VAL* 3.9 11.8 - - - +
153M GLU* 4.6 12.6 + - - +
156M ILE* 3.6 30.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 7 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6M LYS* 1.3 74.1 - - - +
8M ASP* 1.3 81.3 - - - +
9M ASN 3.2 4.7 + - - -
10M GLY 3.2 22.2 + - - +
11M VAL* 3.4 19.5 - - - -
12M ILE* 3.6 33.7 - - + -
116M GLN* 2.9 22.2 + - - -
156M ILE* 3.4 12.0 - - - +
159M THR* 3.3 16.4 - - + +
160M THR 4.1 0.7 - - - +
161M VAL* 3.5 33.9 - - + +
164M ALA* 3.8 18.2 - - + -
190M ILE* 3.1 23.1 - - + +
191M ILE 3.7 3.1 + - - -
192M ASP* 3.1 22.2 + - - +
----------------------------------------------------------
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