Contacts of the strand formed by residues 119 - 123 (chain B) in PDB entry 3FZ7
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 VAL 119 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101B VAL* 4.4 1.8 - - - -
113B PRO* 6.0 2.5 - - + -
117B GLN 4.7 2.7 - - - +
118B ALA* 1.3 73.9 - - - +
120B GLY* 1.3 60.0 + - - +
288B ILE* 3.6 6.1 - - - +
289B TRP* 2.9 48.1 + - + +
291B ASP* 3.5 29.8 - - - +
292B GLU* 3.4 31.2 - - + +
295B LEU* 3.7 34.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 120 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98B LEU* 6.1 0.9 - - - +
101B VAL* 3.8 20.9 - - - +
118B ALA 3.7 3.1 + - - +
119B VAL* 1.3 79.7 - - - +
121B THR* 1.3 65.2 + - - -
287B VAL 3.1 12.6 - - - -
288B ILE* 4.2 0.4 - - - -
289B TRP* 3.7 12.8 - - - -
295B LEU* 5.7 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 121 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84B TRP* 3.7 16.5 - - - -
97B ASP* 5.5 0.2 + - - -
101B VAL* 4.0 6.1 - - - +
120B GLY* 1.3 77.9 - - - -
122B ASN* 1.3 78.7 + - - +
132B LEU* 3.6 21.1 - - + -
286B TRP* 3.5 9.3 - - - -
287B VAL* 2.8 45.3 + - + +
289B TRP* 4.5 5.6 - - + -
312B THR* 6.2 0.2 - - - -
313B PHE* 3.6 28.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 122 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84B TRP* 3.7 12.8 + - - +
97B ASP* 3.3 22.2 + - - +
101B VAL* 4.3 2.4 - - - +
121B THR* 1.3 89.5 + - - +
123B THR* 1.3 67.6 + - - +
128B GLU* 4.9 0.3 - - - +
283B GLY 5.2 0.9 + - - +
284B CYS* 3.5 24.4 - - - +
285B GLY 3.1 17.7 + - - -
286B TRP* 3.5 19.0 - - + -
313B PHE 5.4 0.2 - - - +
314B ALA* 5.8 1.0 - - - +
319B ARG* 2.6 39.3 + - - -
324B VAL* 3.3 17.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 123 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121B THR* 4.2 3.4 - - + +
122B ASN* 1.3 86.1 + - - +
124B ILE* 1.3 56.3 + - - +
125B GLY 2.7 24.6 + - - -
128B GLU* 3.3 33.7 - - + +
129B ALA* 3.6 15.4 - - + +
132B LEU* 3.7 18.4 - - + -
283B GLY 4.0 0.5 - - - +
284B CYS* 3.4 5.2 - - - -
285B GLY 2.6 43.9 + - - +
286B TRP 3.6 0.9 + - - -
287B VAL* 4.3 2.2 - - + -
314B ALA* 6.2 0.2 - - - -
319B ARG* 3.7 9.0 - - - +
----------------------------------------------------------
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