Contacts of the strand formed by residues 146 - 151 (chain A) 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 GLY 146 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140A GLY 3.9 0.5 - - - +
141A HIS* 3.5 17.7 - - - -
142A ASP* 2.9 32.7 + - - +
143A GLU 4.3 3.0 + - - -
144A PHE 3.6 1.8 - - - -
145A ASN* 1.3 80.7 - - - +
147A PHE* 1.3 66.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 147 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41A LYS* 4.1 17.5 + - + +
42A ALA 4.8 2.0 - - - +
43A THR 3.9 12.1 - - - -
44A ASN* 3.6 14.8 - - + -
45A GLY* 3.6 29.2 - - - +
46A VAL* 3.7 16.4 - - + -
140A GLY 3.5 2.9 - - - -
141A HIS* 3.7 33.7 - + + -
145A ASN 3.9 6.4 - - - +
146A GLY* 1.3 75.1 - - - -
147A SER* 1.3 65.5 - - - +
215A ILE* 3.2 27.6 - - + -
216A GLY 3.7 19.5 - - - -
217A ASP* 5.9 0.9 - - - -
220A ARG* 4.4 4.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 147 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41A LYS* 3.9 11.9 - - + +
46A VAL* 3.9 4.4 - - - +
109A THR* 3.7 21.3 - - - +
110A LYS 5.2 0.2 - - - +
138A ILE 4.5 0.4 - - - -
139A ALA* 3.3 5.2 - - - +
140A GLY 3.0 30.8 + - - +
142A ASP* 4.8 2.3 - - - +
145A ASN* 5.1 6.1 - - + +
146A GLY 4.1 5.0 - - - +
147A PHE* 1.3 79.2 - - - +
148A LEU* 1.3 62.9 + - - +
149A TYR* 3.6 24.3 - - + +
159A PRO* 6.2 0.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 148 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39A GLY* 3.4 43.3 - - - +
40A ILE* 4.2 2.5 - - - +
41A LYS* 4.2 7.4 - - + +
46A VAL* 4.3 9.6 - - + -
48A ILE* 4.2 15.9 - - + -
137A LEU* 4.3 15.5 - - + -
138A ILE 3.4 9.9 - - - +
139A ALA* 4.2 4.3 - - + -
147A SER* 1.3 76.7 - - - +
149A TYR* 1.3 70.4 + - - +
159A PRO* 3.3 8.2 - - - +
160A TRP* 3.0 56.2 + - + +
161A LYS 4.3 2.9 - - - +
162A ALA* 4.1 6.5 - - - -
163A THR* 4.3 5.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 149 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109A THR* 3.9 22.2 - - + -
110A LYS* 3.6 30.4 - - + +
113A VAL* 3.7 28.7 - - + -
136A LEU 3.7 0.2 - - - +
137A LEU* 3.2 7.9 - - - +
138A ILE* 2.8 38.1 + - + +
147A SER* 3.6 26.9 - - + +
148A LEU* 1.3 79.4 - - - +
150A GLN* 1.3 61.1 + - - +
151A VAL* 4.9 0.6 - - - +
157A TYR* 4.1 24.7 - + - -
158A PHE 3.4 18.6 - - - -
159A PRO* 3.7 23.7 - - + +
160A TRP* 4.6 1.8 - - - +
63B THR* 4.4 17.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 150 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135A SER* 4.1 2.3 + - - -
136A LEU 3.3 5.4 - - - +
137A LEU* 3.7 16.4 - - + -
149A TYR* 1.3 74.0 - - - +
151A VAL* 1.3 65.2 + - - +
152A ASP* 3.0 30.0 + - - +
157A TYR* 3.0 28.8 - - - +
158A PHE* 3.0 21.2 + - + -
160A TRP* 3.0 41.3 + - + +
163A THR* 4.2 7.3 + - - +
165A ILE* 3.5 24.9 - - + +
----------------------------------------------------------
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