Contacts of the strand formed by residues 129 - 135 (chain B) in PDB entry 1II7
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 TYR 129 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108B GLY 3.6 0.3 - - - +
109B MET* 3.4 8.7 - - - -
110B ARG 2.9 32.1 + - - +
111B LYS 3.3 26.9 - - - -
112B GLU 4.8 0.7 - - - +
113B LYS* 3.5 47.7 - - + +
121B SER* 4.2 15.7 - - - -
122B GLU 3.6 3.4 - - - +
123B ARG* 4.0 35.0 + - + -
124B LEU* 4.8 0.2 - - - -
127B GLY 3.2 18.5 + - - -
128B GLU* 1.3 77.4 - - - +
130B LEU* 1.3 62.1 + - - +
131B VAL* 3.5 6.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 130 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108B GLY* 4.0 10.8 - - - -
109B MET* 4.1 18.8 - - + -
120B THR 3.9 0.9 - - - +
121B SER* 3.5 1.9 - - - -
122B GLU* 2.8 50.8 + - + +
124B LEU* 4.2 15.0 - - + +
129B TYR* 1.3 70.1 - - - +
131B VAL* 1.3 65.5 + - - +
132B LYS* 3.8 26.5 + - + +
142B GLY 4.3 4.9 - - - +
143B MET* 5.5 1.1 - - + -
161B LEU* 3.5 36.1 - - + +
162B PHE* 4.0 24.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 131 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106B VAL 3.9 10.3 - - - +
107B ILE* 3.7 6.0 - - - +
108B GLY* 2.8 41.6 + - - +
110B ARG* 3.5 37.9 - - + +
112B GLU 5.0 0.2 - - - +
114B VAL* 3.9 15.0 - - + -
119B LEU* 3.9 26.7 - - + -
120B THR 3.5 8.3 - - - +
121B SER* 3.8 17.5 - - - +
129B TYR* 4.1 2.9 - - + +
130B LEU* 1.3 78.1 - - - +
132B LYS* 1.3 65.4 + - - +
142B GLY 4.4 2.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 132 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107B ILE* 4.3 0.4 - - - -
119B LEU* 3.4 8.2 - - - +
120B THR* 3.0 45.9 + - + +
122B GLU* 2.9 29.8 + - + +
130B LEU* 3.8 25.0 - - + +
131B VAL* 1.3 78.2 - - - +
133B GLY* 1.3 65.6 + - - +
134B VAL* 5.3 0.2 - - + -
139B GLU* 4.3 7.7 + - - +
140B ILE 3.6 8.5 - - - +
141B HIS* 3.4 50.9 + - + +
142B GLY 5.6 0.2 - - - +
161B LEU 4.7 6.5 + - - -
162B PHE* 5.1 0.9 - - + -
163B ARG* 4.6 7.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 133 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79B PHE* 3.7 16.6 - - - -
107B ILE* 3.6 11.4 - - - +
118B TYR 3.3 8.1 - - - -
119B LEU* 3.8 2.7 - - - -
132B LYS* 1.3 73.9 - - - +
134B VAL* 1.3 62.4 + - - +
139B GLU* 3.4 6.6 - - - +
140B ILE* 2.8 41.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 134 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79B PHE* 3.8 3.8 - - - -
116B ASN 5.7 0.7 - - - +
117B GLU 3.6 8.9 - - - +
118B TYR* 2.7 45.7 + - - +
119B LEU 4.6 0.7 - - - -
120B THR* 3.5 37.2 - - + +
132B LYS 4.0 1.3 - - - +
133B GLY* 1.3 81.9 - - - +
135B TYR* 1.3 64.6 + - - +
136B LYS 3.8 19.3 - - - +
138B LEU 3.7 4.5 - - - +
139B GLU* 4.7 12.8 - - + +
140B ILE* 5.1 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 135 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1B MET* 3.8 23.0 - - + +
42B ASP* 3.5 48.9 + - + +
43B PHE* 3.7 25.1 - + + -
77B PRO* 3.9 17.0 - - + -
79B PHE* 4.7 5.2 - + + -
118B TYR* 3.8 25.8 - + - -
133B GLY 4.3 0.2 - - - -
134B VAL* 1.3 73.7 - - - +
136B LYS* 1.3 107.0 + - + +
138B LEU* 2.9 29.5 + - + +
140B ILE* 4.8 4.9 - - + +
----------------------------------------------------------
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