Contacts of the strand formed by residues 108 - 112 (chain B) in PDB entry 3EQ6
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 ARG 108 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106B GLY 4.0 5.5 + - - +
107B ASP* 1.3 76.1 - - - +
109B VAL* 1.3 65.8 + - - +
110B ALA 4.1 0.7 - - - -
132B ILE* 3.3 27.2 - - + +
134B MET* 3.7 18.8 - - - -
151B MET 4.8 1.6 + - - -
152B SER* 2.8 45.1 + - - +
153B LYS* 4.9 3.7 + - - +
154B ALA* 3.6 11.7 - - - -
155B LYS* 3.0 29.2 + - - +
156B ALA 3.5 4.7 + - - -
218B ILE* 3.9 23.3 - - - +
230B MET* 4.8 1.6 - - - -
232B GLU* 5.0 4.0 + - - -
427B VAL* 3.7 28.1 - - - +
428B ASP* 5.1 4.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 109 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97B LEU* 4.9 4.3 - - + -
103B LEU* 4.1 15.3 - - + -
107B ASP 4.6 2.0 - - - +
108B ARG* 1.3 80.7 - - - +
110B ALA* 1.3 73.2 + - - +
111B VAL* 3.5 13.2 - - + +
126B CYS* 4.3 14.1 - - - -
131B LEU* 4.2 26.2 - - + -
132B ILE 2.8 10.8 + - - +
133B PHE* 3.6 0.5 - - - -
134B MET* 2.8 28.9 + - - -
156B ALA* 3.5 26.7 - - + -
158B VAL* 4.1 14.6 - - + -
----------------------------------------------------------
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
----------------------------------------------------------
109B VAL* 1.3 75.3 - - - +
111B VAL* 1.3 61.5 + - - +
112B VAL* 4.2 4.5 - - + -
134B MET* 3.6 24.3 - - + +
148B ARG* 6.4 1.8 - - + -
149B LEU* 3.9 24.2 - - + -
156B ALA 2.9 14.4 + - - +
157B ILE* 3.3 14.7 - - + -
158B VAL 2.8 25.7 + - - -
----------------------------------------------------------
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
----------------------------------------------------------
109B VAL* 3.5 22.4 - - + +
110B ALA* 1.3 80.9 - - - +
112B VAL* 1.3 61.8 + - - +
113B LEU* 3.9 17.8 + - + -
119B TRP* 3.9 28.2 + - + +
122B VAL* 4.2 22.9 - - + -
123B ILE* 4.4 15.0 - - + -
126B CYS* 5.1 0.2 - - - -
133B PHE* 4.6 3.4 - - + -
134B MET 3.1 13.0 + - - +
135B PRO* 3.4 8.0 - - + +
136B GLY 3.0 26.2 + - - +
158B VAL* 3.4 5.8 - - + +
----------------------------------------------------------
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
----------------------------------------------------------
110B ALA* 4.9 3.4 - - + -
111B VAL* 1.3 80.8 - - - +
113B LEU* 1.3 58.8 + - - +
134B MET 5.5 0.2 - - - +
136B GLY 3.7 5.2 - - - +
137B THR 3.4 33.4 - - - +
138B ILE* 3.8 13.3 - - - +
140B MET* 3.7 22.4 - - + -
145B ILE* 5.2 3.4 - - + -
157B ILE* 4.2 21.5 - - + -
158B VAL 2.8 10.1 + - - +
159B ALA* 3.5 18.7 - - + +
160B GLY 3.5 5.0 + - - -
163B VAL* 3.8 23.7 - - + +
----------------------------------------------------------
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