Contacts of the strand formed by residues 121 - 127 (chain B) in PDB entry 3JTC
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 SER 121 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117B ALA* 3.3 3.8 - - - -
118B VAL* 3.0 30.8 + - - +
119B ASN 3.3 3.3 + - - -
120B GLY* 1.4 77.3 - - - +
122B SER* 1.3 71.5 + - - +
123B PHE* 4.1 0.7 - - - +
138B GLN* 5.6 5.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 122 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96B ARG* 5.4 4.3 - - - +
116B VAL 4.1 5.2 - - - -
117B ALA* 4.3 5.1 - - - +
120B GLY 4.3 1.0 + - - -
121B SER* 1.3 78.6 - - - +
123B PHE* 1.3 59.7 + - - +
136B ASP* 3.3 31.7 + - - +
137B THR* 3.6 18.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 123 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116B VAL* 2.9 21.5 + - + +
118B VAL* 3.6 36.1 - - + +
121B SER 4.1 0.7 - - - +
122B SER* 1.3 76.2 - - - +
124B VAL* 1.3 79.7 + - + +
135B ALA* 3.7 1.9 - - - +
136B ASP* 2.8 27.2 + - - +
137B THR* 3.4 23.3 + - + +
143B VAL* 4.1 18.2 - - + -
144B VAL* 3.6 27.5 - - + +
147B THR* 3.9 29.4 - - + -
607B PTY 3.9 25.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 124 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115B GLU* 3.9 0.3 - - - +
116B VAL* 2.9 46.5 + - + +
123B PHE* 1.3 105.9 - - + +
125B SER* 1.3 59.2 + - - +
133B TRP* 3.8 18.8 - - + -
134B GLN 3.2 10.1 - - - +
136B ASP* 3.0 12.1 - - - +
144B VAL* 4.3 7.2 - - + -
147B THR* 4.8 4.5 - - + -
148B LEU* 3.6 30.7 - - + -
151B LEU* 4.1 11.2 - - + -
607B PTY 5.0 1.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 125 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114B PHE 3.3 11.7 - - - -
115B GLU* 4.1 16.2 - - - -
124B VAL* 1.3 73.3 - - - +
126B PHE* 1.3 64.2 + - - +
127B ARG* 3.3 30.8 + - - -
133B TRP* 3.4 7.7 - - - -
134B GLN* 2.9 32.1 + - - -
136B ASP* 2.8 24.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 126 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112B VAL* 5.5 0.2 - - + -
113B PHE* 5.0 2.8 - - - -
114B PHE* 2.9 33.9 + - + +
125B SER* 1.3 74.7 - - - +
127B ARG* 1.3 75.5 + - - +
128B PRO* 3.5 32.5 - - + +
131B ALA* 3.6 34.5 - - + -
132B LEU 3.8 2.2 - - - -
133B TRP* 3.5 37.9 - + + -
157B THR 4.0 1.6 - - - -
158B ARG 3.5 22.7 - - - -
161B LEU* 3.7 22.7 - - + -
162B ARG* 3.9 16.2 - - + -
165B LEU* 4.0 14.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 127 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115B GLU* 5.7 2.8 + - - +
125B SER* 3.3 31.4 + - - +
126B PHE* 1.3 85.6 + - - +
128B PRO* 1.3 70.9 - - - +
129B GLU* 3.2 17.0 + - - +
130B ARG 3.9 2.6 + - - +
131B ALA* 3.1 16.5 + - - -
132B LEU* 2.8 26.0 + - + +
134B GLN* 2.6 58.3 + - + +
136B ASP* 5.0 3.4 + - - -
----------------------------------------------------------
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