Contacts of the strand formed by residues 219 - 227 (chain A) in PDB entry 5MJ3
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 LYS 219 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82A PHE* 3.8 26.2 - - + -
104A LEU 3.7 6.3 - - - +
106A LYS* 4.0 19.1 - - + +
113A SER* 4.9 0.4 - - - +
115A ASP* 2.9 32.3 + - + +
116A ILE* 3.9 10.3 - - + +
214A ALA 3.7 1.0 - - - +
215A VAL* 3.2 7.2 - - - -
216A HIS* 2.9 46.9 + - + +
217A LYS* 3.5 0.6 - - - +
218A LEU* 1.3 76.5 - - - +
220A TYR* 1.3 67.5 + - - +
221A GLU* 3.7 24.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 220 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24A TRP* 3.6 17.8 - + - -
26A LEU* 3.7 20.9 - - + -
32A VAL* 3.8 12.3 - - + -
103A LEU* 4.1 19.1 - - + -
104A LEU 2.9 20.6 + - - +
105A HIS* 3.1 48.3 - + - -
106A LYS 4.6 0.7 + - - -
213A ASP* 2.6 39.0 + - + -
214A ALA 3.5 2.2 - - - -
215A VAL* 4.0 17.3 - - + -
218A LEU 3.8 1.0 + - - -
219A LYS* 1.3 74.1 - - - +
221A GLU* 1.3 77.8 + - - +
222A ASN* 2.9 24.8 + - - -
1D NAG 3.5 11.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 221 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105A HIS* 4.0 7.2 - - + -
113A SER* 2.7 43.3 + - - +
115A ASP* 2.8 24.8 + - - +
116A ILE* 2.8 30.8 + - + +
213A ASP* 3.7 1.4 - - - -
214A ALA 2.9 32.2 + - - +
219A LYS* 3.7 6.4 - - + +
220A TYR* 1.3 87.6 - - - +
222A ASN* 1.3 65.1 + - - +
223A TYR* 2.6 36.4 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 222 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105A HIS* 4.3 8.5 + - - -
112A TRP* 6.1 1.2 - - - +
113A SER 5.3 1.1 + - - +
114A THR* 5.3 3.5 - - - +
211A MET* 6.6 0.2 - - + -
212A VAL 3.1 13.7 - - - +
213A ASP* 3.7 5.2 - - - +
220A TYR* 2.9 15.6 + - - +
221A GLU* 1.3 79.0 - - - +
223A TYR* 1.3 76.4 + - - +
224A THR* 5.2 5.5 - - - +
1D NAG 1.4 63.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 223 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114A THR* 3.3 27.2 - - + -
117A LEU* 3.2 40.3 + - + -
128A PHE* 3.7 42.0 - + + -
129A LEU* 4.0 22.0 - - + -
211A MET* 3.5 0.7 - - - +
212A VAL* 2.9 37.1 + - + +
214A ALA* 4.1 13.2 - - + -
221A GLU* 2.6 42.9 + - + -
222A ASN* 1.3 81.9 + - - +
224A THR* 1.3 70.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 224 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129A LEU* 3.8 8.3 + - - +
209A GLU* 5.4 5.2 - - - -
210A VAL 3.1 8.1 - - - -
211A MET* 4.1 19.5 - - + -
222A ASN* 5.2 6.7 - - - +
223A TYR* 1.3 83.4 - - - +
225A SER* 1.3 65.0 + - - +
1D NAG 6.0 2.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 225 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129A LEU* 4.0 29.3 + - - +
131A CYS* 4.7 5.2 + - - -
208A ILE 3.8 0.5 - - - +
209A GLU* 3.5 4.9 - - - +
210A VAL* 2.8 37.3 + - - +
224A THR* 1.3 75.4 - - - +
226A SER* 1.3 63.3 + - - +
227A PHE* 3.7 22.5 - - - -
54B MET* 4.6 14.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 226 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207A PRO* 3.5 14.4 - - - +
208A ILE 3.2 4.9 - - - -
209A GLU* 2.8 34.7 + - - -
225A SER* 1.3 74.4 + - - +
227A PHE* 1.3 68.4 + - - +
53B HIS* 5.2 0.3 + - - -
54B MET* 4.8 18.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 227 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131A CYS* 3.6 33.4 - - + -
140A PHE* 3.9 12.1 - + - -
207A PRO* 3.9 7.8 - - - +
208A ILE* 2.7 64.3 + - + +
210A VAL* 3.8 18.4 - - + -
225A SER* 3.7 18.4 - - - -
226A SER* 1.3 81.0 + - - +
228A PHE* 1.3 69.9 + - - +
229A ILE* 4.8 2.0 - - + -
232A ILE* 3.4 39.9 - - + -
53B HIS* 4.2 14.8 - - + -
----------------------------------------------------------
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