Contacts of the strand formed by residues 108 - 113 (chain L) in PDB entry 4IBL
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 THR 108 (chain L).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105L HIS* 2.3 47.9 + - + +
106L THR 3.0 8.0 - - - +
107L GLY* 1.3 81.7 + - - +
109L LYS* 1.3 72.7 + - - +
110L ARG 3.6 1.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 109 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89L LEU* 4.0 28.7 - - + +
105L HIS* 3.3 15.9 + - - +
108L THR* 1.3 88.1 + - - +
110L ARG* 1.3 86.9 + - - +
111L SER* 4.9 0.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 110 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89L LEU* 3.7 48.4 + - + +
91L CYS* 5.0 0.2 - - - -
96L GLY* 2.9 27.4 + - - +
97L GLY* 4.9 0.6 - - - -
98L CYS* 3.7 12.5 - - - -
102L CYS* 3.8 9.6 - - - -
103L SER 3.1 18.6 - - - +
104L ASP* 4.2 11.7 - - - +
105L HIS* 4.0 5.8 - - - +
108L THR 3.6 2.6 + - - -
109L LYS* 1.3 102.1 - - - +
111L SER* 1.3 75.0 + - - +
112L CYS* 3.8 10.9 - - - +
124L GLY 5.0 2.4 + - - -
125L VAL* 3.5 22.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 111 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102L CYS* 3.6 2.8 - - - -
103L SER* 2.8 36.7 + - - +
105L HIS* 2.8 27.6 + - - -
109L LYS 4.9 0.4 - - - -
110L ARG* 1.3 85.9 - - - +
112L CYS* 1.3 66.7 + - - +
113L ARG* 5.0 5.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 112 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98L CYS* 2.1 54.1 - - + -
101L TYR 3.2 4.3 - - - -
110L ARG* 3.7 10.5 - - - -
111L SER* 1.3 78.3 - - - +
113L ARG* 1.3 68.5 + - - +
120L LEU* 3.7 22.1 - - + +
124L GLY 3.2 25.8 + - - +
125L VAL* 3.7 21.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 113 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125H GLU* 2.8 43.0 + - - -
127H THR* 5.7 1.0 + - - -
100L GLN* 4.3 1.0 + - - -
101L TYR* 2.8 44.6 + - + +
102L CYS 4.1 7.5 + - - -
103L SER* 2.8 32.4 + - - +
111L SER* 5.0 6.7 - - - +
112L CYS* 1.3 81.3 - - - +
114L CYS* 1.3 72.5 + - - +
120L LEU* 4.8 3.1 - - - -
127L CYS* 3.7 4.3 - - - -
----------------------------------------------------------
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