Contacts of the strand formed by residues 107 - 113 (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 LYS 107 (chain X).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104X TYR* 3.8 5.7 - - - -
105X ASP* 3.0 57.4 + - - +
106X ASN* 1.3 82.2 - - - +
108X PRO* 1.3 76.1 - - + +
109X GLU* 4.1 5.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 108 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7X ARG* 3.6 16.0 + - + -
8X VAL 3.7 13.2 - - - +
9X GLN 3.5 27.8 - - - +
10X ASP 3.8 0.4 - - - -
11X SER* 3.5 25.8 - - - +
12X VAL* 3.5 20.9 - - + +
103X GLY 3.5 5.6 - - - +
104X TYR* 3.9 14.3 - - + -
106X ASN 4.7 0.7 - - - +
107X LYS* 1.3 91.1 - - + +
109X GLU* 1.3 64.5 + - - +
121X GLU* 5.3 0.2 - - - +
178X VAL 5.0 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 109 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7X ARG* 4.6 2.5 - - - +
12X VAL* 3.5 4.6 - - - +
76X PRO* 3.4 24.6 - - + +
77X GLN* 3.6 14.3 + - - +
101X ILE 3.5 1.6 - - - +
102X GLY* 3.4 4.7 - - - -
103X GLY 2.8 38.5 + - - +
105X ASP* 4.2 33.7 + - - +
107X LYS* 4.1 10.4 - - + +
108X PRO* 1.3 81.4 - - - +
110X LEU* 1.3 60.5 + - - +
111X TYR* 3.6 28.0 + - + -
121X GLU* 4.8 10.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 110 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5X GLY* 3.3 33.4 - - - +
6X ILE* 3.7 5.4 - - - +
7X ARG* 4.2 8.3 - - + +
12X VAL* 3.8 21.7 - - + +
14X LEU* 3.9 20.0 - - + -
100X LEU* 4.4 12.6 - - + -
101X ILE 3.4 13.2 - - - +
109X GLU* 1.3 75.2 - - - +
111X TYR* 1.3 65.7 + - - +
112X GLN* 6.1 0.7 - - + -
121X GLU* 3.4 12.4 + - - +
122X LEU* 3.1 38.0 + - + +
123X PRO 4.2 0.9 - - - +
124X TYR* 3.8 9.6 - - - +
125X GLY* 3.7 15.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 111 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76X PRO* 3.9 6.3 - - + -
77X GLN* 3.3 48.9 - - + +
80X SER* 3.7 28.7 - - - -
99X VAL 4.0 0.2 - - - +
100X LEU* 3.3 8.5 - - - +
101X ILE* 2.8 52.2 + - + +
109X GLU* 3.6 32.8 + - + -
110X LEU* 1.3 76.1 - - - +
112X GLN* 1.3 60.9 + - - +
113X ILE* 4.2 8.1 + - + +
119X LYS* 4.0 19.7 - - + -
120X VAL 3.6 6.1 - - - +
121X GLU* 3.6 32.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 112 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27W VAL* 3.4 24.7 - - - +
100X LEU* 3.5 9.5 - - + +
110X LEU* 4.2 1.5 - - + -
111X TYR* 1.3 72.0 - - - +
113X ILE* 1.3 65.8 + - - +
118X THR 3.3 3.5 - - - +
120X VAL* 2.9 42.0 + - + +
122X LEU* 3.7 19.3 - - + +
125X GLY* 3.1 13.5 - - - -
126X ALA 2.8 45.8 + - - +
127X HIS* 3.5 22.4 - - + +
135X PHE* 4.2 2.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 113 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80X SER* 3.8 24.2 - - - +
83X VAL* 4.1 8.3 - - + -
84X ARG* 4.3 8.3 - - + +
87X LEU* 3.7 15.7 - - + +
97X VAL 4.7 0.2 - - - +
99X VAL* 2.8 48.8 + - + +
101X ILE* 3.8 25.6 - - + -
111X TYR* 4.6 2.5 - - + -
112X GLN* 1.3 84.5 - - - +
114X ASP* 1.3 71.0 + - - +
117X GLY* 4.2 8.3 - - - -
118X THR 3.1 14.8 - - - +
119X LYS* 3.7 21.3 - - + -
127X HIS* 3.1 5.3 + - - -
----------------------------------------------------------
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