Contacts of the strand formed by residues 104 - 112 (chain B) in PDB entry 1S9C
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 104 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21B ALA* 3.2 2.1 - - - -
22B TYR* 2.8 54.1 + - - -
101B PRO* 4.9 3.1 - - - -
103B ALA* 1.3 77.1 - - - +
105B LYS* 1.3 64.4 + - - -
106B LEU* 4.9 1.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 105 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20B TYR 3.4 3.8 - - - +
21B ALA* 3.4 23.1 - - + -
104B GLY* 1.3 73.9 - - - -
106B LEU* 1.3 74.6 + - - +
132B SER* 3.6 15.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 106 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19B SER* 3.3 7.4 - - - -
20B TYR 2.6 42.3 + - - +
22B TYR* 3.8 18.4 - - + +
64B ILE* 3.4 47.1 - - + -
100B LEU* 5.4 2.9 - - + -
101B PRO* 5.5 4.9 - - + -
104B GLY* 4.9 0.7 - - - -
105B LYS* 1.3 80.6 - - - +
107B LYS* 1.3 60.8 + - - +
108B CYS* 4.6 1.3 - - - -
130B SER* 4.7 6.1 - - - -
131B TYR 3.1 12.3 - - - +
132B SER* 3.3 32.3 - - - +
137B ILE* 3.4 21.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 107 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17B PRO* 5.1 9.6 - - + -
18B PHE 4.1 4.9 - - - +
19B SER* 4.3 5.6 - - - +
106B LEU* 1.3 73.0 - - - +
108B CYS* 1.3 63.9 + - - +
109B GLU* 3.3 29.4 + - + +
130B SER* 3.3 0.3 - - - -
131B TYR* 2.6 55.8 + - + +
132B SER* 5.0 0.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 108 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17B PRO* 3.5 3.8 - - - +
18B PHE* 2.8 74.1 + - + +
20B TYR* 4.4 5.8 - - - -
64B ILE* 3.9 17.3 - - - -
106B LEU 4.4 8.3 - - - -
107B LYS* 1.3 77.0 - - - +
109B GLU* 1.3 68.8 + - - +
110B ALA 4.2 0.7 - - - -
128B VAL* 4.6 2.5 - - + -
129B TYR 3.2 6.3 - - - +
130B SER* 3.3 26.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 109 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15B LEU 5.7 0.7 - - - +
17B PRO* 4.4 16.2 - - + -
107B LYS* 3.3 29.5 + - - -
108B CYS* 1.3 79.7 - - - +
110B ALA* 1.3 62.6 + - - +
111B VAL* 3.9 6.9 + - + +
128B VAL* 3.3 3.5 - - - -
129B TYR* 2.7 43.8 + - + +
131B TYR* 3.6 32.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 110 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14B LYS 3.7 0.3 - - - -
15B LEU* 3.2 43.2 + - + +
16B PRO 5.0 5.5 + - - +
18B PHE* 4.4 16.2 - - + -
68B SER* 6.0 3.1 - - - -
108B CYS 4.2 1.0 - - - -
109B GLU* 1.3 73.3 - - - +
111B VAL* 1.3 65.1 + - - +
126B MET* 4.1 19.1 - - + -
127B ASP 3.7 5.2 - - - -
128B VAL* 4.1 11.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 111 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12B GLY 4.3 3.4 - - - +
13B GLN 4.3 2.9 - - - -
14B LYS* 3.9 32.3 - - + +
15B LEU 4.5 0.2 - - - +
109B GLU* 4.3 13.2 - - + +
110B ALA* 1.3 80.6 - - - +
112B VAL* 1.3 76.9 + - - +
113B ALA* 3.2 2.1 + - + -
126B MET* 3.4 3.1 - - - +
127B ASP* 2.8 40.3 + - + +
129B TYR* 5.1 11.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 112 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12B GLY* 3.5 24.0 - - - +
13B GLN* 3.3 26.5 + - + +
15B LEU* 3.4 27.8 - - + +
111B VAL* 1.3 79.6 - - - +
113B ALA* 1.3 61.1 + - - +
114B ASP 3.7 20.9 - - - +
115B VAL* 4.9 6.7 - - + -
124B ILE* 5.1 13.9 - - + -
125B ILE 4.0 4.5 - - - +
126B MET* 3.9 12.3 - - + -
----------------------------------------------------------
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