Contacts of the strand formed by residues 147 - 155 (chain A) in PDB entry 2JG7
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 HIS 147 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142A SER* 3.4 27.6 + - - +
144A ARG* 3.3 40.3 + - + +
145A PRO* 2.9 23.8 + - + -
146A GLY* 1.3 79.4 + - - +
148A ALA* 1.3 58.7 + - - +
494A THR* 3.8 18.2 - - + -
495A ILE 3.2 4.0 - - - +
496A ASN* 3.4 39.1 - - + +
497A TYR* 3.5 6.9 + - - -
498A SER* 4.5 3.4 - - - -
500A ASP* 6.0 2.0 - - + -
456B ILE* 3.8 15.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 148 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139A VAL* 6.3 1.1 - - + -
142A SER* 4.7 0.9 - - - -
147A HIS* 1.3 73.6 - - - +
149A LEU* 1.3 61.2 + - - +
150A ILE* 4.2 7.2 - - + -
493A CYS 3.7 0.5 - - - +
494A THR* 3.3 4.5 - - - +
495A ILE* 2.7 52.7 + - + +
497A TYR* 3.5 4.5 - - + -
439C PHE* 3.7 35.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 149 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139A VAL* 3.9 2.0 - - - +
140A LEU* 2.8 72.2 + - + +
141A PRO 4.5 2.0 - - - +
142A SER* 4.0 14.6 - - - -
147A HIS 4.1 1.2 + - - -
148A ALA* 1.3 74.0 - - - +
150A ILE* 1.3 62.2 + - - +
492A THR* 3.9 25.1 - - + -
493A CYS 3.3 15.0 - - - +
494A THR* 3.4 18.6 - - - +
462B GLU* 3.8 33.7 - - + +
464B GLY* 4.9 3.1 - - - -
465B GLY* 4.5 8.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 150 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138A PRO 3.9 3.8 - - - -
139A VAL* 4.0 24.2 - - + -
140A LEU* 4.6 2.7 - - - +
148A ALA* 4.2 7.8 - - + -
149A LEU* 1.3 86.3 - - - +
151A GLU* 1.3 58.1 + - - +
152A GLN* 3.8 29.4 - - + +
491A SER 3.7 0.2 - - - +
492A THR* 3.8 1.5 - - - -
493A CYS* 2.8 51.3 + - + +
495A ILE* 4.9 8.1 - - + -
439B PHE* 5.5 6.7 - - + -
442B LEU* 4.0 18.8 - - + -
439C PHE* 6.2 1.6 - - + -
139D VAL* 4.1 15.9 - - + -
150D ILE* 5.5 9.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 151 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137A GLY* 3.5 21.9 + - - +
138A PRO* 3.0 38.0 + - + +
140A LEU* 5.0 6.6 - - + +
150A ILE* 1.3 72.4 - - - +
152A GLN* 1.3 62.2 + - - +
153A TRP* 2.8 26.2 + - - +
485A LYS* 5.6 1.4 + - - -
490A ARG* 2.6 41.8 + - + -
491A SER 3.5 5.6 - - - +
492A THR* 4.8 4.9 - - + +
466B ALA* 4.5 1.9 + - - +
481B SER* 2.6 31.8 + - - -
482B ASP* 5.8 0.2 - - - -
139D VAL* 3.9 9.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 152 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
150A ILE* 3.8 24.8 + - + +
151A GLU* 1.3 73.2 - - - +
153A TRP* 1.3 69.5 + - - +
154A ASN* 4.2 9.1 + - - +
489A ARG 3.5 0.9 - - - +
490A ARG* 3.4 4.9 - - - +
491A SER* 2.8 51.0 + - - +
493A CYS* 4.0 10.1 - - - -
442B LEU* 3.3 33.0 + - + +
443B GLY* 4.4 4.8 - - - -
139D VAL* 3.5 27.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 153 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136A GLY* 3.4 12.8 + - - +
137A GLY* 3.3 28.9 - - - +
151A GLU* 2.8 23.3 + - - -
152A GLN* 1.3 82.5 + - - +
154A ASN* 1.3 69.0 + - - +
484A TRP* 3.7 23.7 - + + -
485A LYS* 3.6 49.4 - - + +
488A MET* 3.7 33.9 - - + +
489A ARG 3.5 2.5 - - - -
490A ARG* 3.5 67.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 154 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152A GLN* 4.2 12.2 + - - +
153A TRP* 1.3 80.3 + - - +
155A PRO* 1.4 70.3 - - + +
488A MET* 3.2 9.1 - - - +
489A ARG* 2.8 65.9 + - + +
491A SER* 4.5 3.0 + - - -
442B LEU 3.2 23.8 + - - -
443B GLY* 3.3 5.9 + - - -
444B PRO* 3.0 35.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 155 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70A TRP* 3.8 21.5 - - + +
74A ALA* 4.6 3.1 - - + -
81A ARG* 4.5 8.7 - - - +
153A TRP 4.9 0.2 - - - +
154A ASN* 1.4 96.2 - - + +
156A VAL* 1.3 61.4 + - - +
182A CYS 3.2 21.1 - - - +
183A GLY* 3.2 29.8 - - - +
184A ASN* 3.3 11.2 - - - +
487A TYR 4.2 3.6 - - - +
488A MET* 3.7 4.0 - - + -
489A ARG* 3.9 14.0 + - - -
444B PRO* 4.1 13.9 - - + -
----------------------------------------------------------
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