Contacts of the strand formed by residues 122 - 129 (chain D) in PDB entry 2J2M
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 GLY 122 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12B GLN 3.2 14.6 - - - -
13B GLY* 3.5 12.5 + - - -
14B VAL* 3.8 3.6 - - - -
119D THR* 2.9 36.5 + - - +
120D GLU 3.6 0.4 - - - -
121D GLU* 1.3 78.7 - - - +
123D ASN* 1.3 67.4 + - - -
321D VAL* 3.4 2.7 - - - +
359D PRO* 5.2 0.7 - - - -
361D ALA* 4.0 3.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 123 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12B GLN* 2.8 28.8 + - - +
14B VAL* 4.5 3.3 - - - +
116D LYS* 4.0 17.7 - - + +
117D PHE 3.3 4.5 - - - +
118D TYR* 3.5 28.0 - - - -
122D GLY* 1.3 74.8 - - - -
124D TRP* 1.3 60.8 + - - +
319D VAL* 3.2 22.8 - - + +
320D LEU 4.2 2.8 - - - +
321D VAL* 3.8 6.9 - - - +
357D ASN 3.1 27.1 + - - -
358D CYS 3.7 3.4 + - - -
359D PRO* 3.4 30.8 - - - +
360D PHE 3.9 1.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 124 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80D PHE* 3.7 28.5 - + + -
81D LEU* 5.5 0.9 - - + -
116D LYS* 3.5 0.7 - - - -
117D PHE* 2.7 88.7 + + + -
119D THR* 5.3 0.7 - - - +
122D GLY 3.7 0.6 + - - -
123D ASN* 1.3 74.0 - - - +
125D ASP* 1.3 78.4 + - - +
126D PHE* 4.2 13.7 - + + +
201D PHE* 6.0 0.2 - - - -
203D TRP* 5.3 3.1 - + - -
215D LEU* 3.7 33.0 - - + -
217D TRP* 6.0 0.7 - + - -
260D LEU* 5.0 10.3 - - + -
319D VAL 3.1 18.4 - - - -
320D LEU* 3.5 26.0 - - + +
321D VAL* 3.9 19.1 - - + +
324D MET* 3.9 22.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 125 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12B GLN* 5.0 0.9 + - - +
115D VAL 3.4 2.5 - - - -
116D LYS* 2.9 51.4 + - - +
123D ASN* 4.9 0.3 - - - +
124D TRP* 1.3 87.0 + - - +
126D PHE* 1.3 60.7 + - - +
127D VAL* 3.9 0.4 - - + -
314D GLY 3.7 0.5 - - - +
315D PHE* 3.3 14.3 - - + -
316D ASN 3.1 45.0 + - - +
317D PRO* 3.8 9.9 - - - +
319D VAL* 2.9 25.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 126 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113D PHE* 3.1 30.7 - + + -
114D SER* 3.2 2.4 - - - -
115D VAL* 2.8 43.6 + - + +
117D PHE* 4.1 16.4 - - + -
124D TRP* 4.0 12.0 + + + +
125D ASP* 1.3 71.5 - - - +
127D VAL* 1.3 62.0 + - - +
128D GLY* 3.5 8.1 - - - -
196D SER 3.5 23.8 - - - -
197D SER* 3.8 22.7 - - - -
215D LEU* 3.9 29.2 - - + -
217D TRP* 3.3 40.6 - + - -
260D LEU* 5.7 0.2 - - + -
315D PHE* 4.8 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 127 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113D PHE 3.9 2.0 - - - -
114D SER* 3.4 17.3 - - - +
125D ASP* 3.9 3.5 + - + -
126D PHE* 1.3 79.7 - - - +
128D GLY* 1.3 57.7 + - - +
197D SER* 4.7 4.0 - - - +
201D PHE* 6.1 0.4 - - - -
315D PHE* 3.4 27.4 - - + -
316D ASN 3.7 2.7 - - - -
317D PRO* 3.5 31.6 - - + +
335D ARG* 2.8 48.2 + - - +
339D TYR* 3.9 11.7 - - + -
501D HEM 3.7 21.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 128 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113D PHE* 2.7 41.0 + - - -
126D PHE* 3.5 7.3 - - - -
127D VAL* 1.3 74.7 - - - +
129D ASN* 1.3 58.7 + - - -
196D SER 3.1 17.5 - - - -
197D SER* 4.7 2.0 - - - -
501D HEM 3.3 21.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 129 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56D HIS* 3.5 15.1 + - - -
97D VAL* 5.2 0.4 - - - +
110D PRO* 4.0 19.2 - - + +
111D ARG 2.9 9.8 - - - +
112D GLY* 3.3 20.6 + - - -
113D PHE* 4.2 2.5 - - - +
128D GLY* 1.3 73.4 - - - +
130D ASN* 1.3 60.2 + - - +
131D LEU* 3.8 15.7 - - - +
133D VAL 5.5 0.2 + - - -
134D PHE* 4.0 20.2 - - - -
176D MET* 5.2 1.4 - - - +
195D GLY* 3.4 3.6 - - - -
196D SER* 2.6 38.3 + - - +
198D VAL* 4.6 1.5 - - + +
501D HEM 3.4 30.4 - - + +
----------------------------------------------------------
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