Contacts of the strand formed by residues 218 - 225 (chain B) in PDB entry 3RLQ
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 ILE 218 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
225A GLU* 2.5 17.1 - - - +
226A LEU* 3.0 30.1 + - + +
229A HIS* 3.2 42.2 + - + +
49B ILE* 4.3 17.7 - - + -
78B ILE* 3.2 19.1 - - + +
80B LEU* 3.8 31.6 - - + -
207B VAL* 4.1 11.7 - - + -
211B SER* 4.2 2.9 - - - +
214B ILE* 4.1 16.2 - - + -
216B TYR 3.7 7.4 - - - +
217B PRO* 1.3 76.4 - - - +
219B THR* 1.3 57.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 219 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
223A GLU* 3.6 38.2 + - + +
224A LYS 3.6 10.3 - - - +
225A GLU* 2.5 30.3 + - + +
226A LEU* 4.8 1.1 - - - -
77B HIS* 5.8 1.2 - - - +
78B ILE 2.8 10.0 + - - -
79B ASN* 3.2 19.3 + - - -
80B LEU* 2.8 32.3 + - - +
217B PRO* 4.6 3.3 - - - +
218B ILE* 1.3 74.8 + - - +
220B LEU* 1.3 58.9 + - - +
221B PHE* 3.6 12.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 220 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
222A VAL 3.3 1.1 - - - +
223A GLU* 3.3 3.1 - - - -
224A LYS* 2.8 68.1 + - + +
226A LEU* 3.9 20.3 - - + +
80B LEU* 3.4 13.2 - - + +
82B PRO* 3.4 37.9 - - + -
200B GLU* 4.0 29.2 - - + +
203B ILE* 4.0 17.9 - - + -
204B LYS* 4.4 6.3 - - + -
218B ILE 4.3 0.4 + - - -
219B THR* 1.3 72.5 - - - +
221B PHE* 1.3 61.0 + - - +
222B VAL* 4.0 6.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 221 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81A ILE* 4.3 12.6 - - + -
221A PHE* 4.1 30.3 - + + -
222A VAL 3.3 5.2 - - - -
223A GLU* 3.3 48.7 - - + -
79B ASN* 3.4 41.7 - - + -
80B LEU 2.9 9.9 + - - -
81B ILE* 3.4 21.7 - - + +
82B PRO* 3.2 18.0 - - - +
219B THR* 3.6 17.3 - - + -
220B LEU* 1.3 73.2 - - - +
222B VAL* 1.3 63.4 + - - +
223B GLU 3.4 2.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 222 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
220A LEU 3.4 1.6 - - - +
221A PHE* 3.4 2.9 - - - -
222A VAL* 2.9 47.5 + - + +
224A LYS* 4.3 10.1 - - + +
82B PRO* 4.1 13.0 - - + +
84B LYS* 6.4 3.1 - - + -
198B LEU 5.5 3.4 - - - +
200B GLU* 4.2 17.9 - - + +
220B LEU* 4.0 28.0 - - + -
221B PHE* 1.3 72.5 - - - +
223B GLU* 1.3 62.5 + - - +
224B LYS* 3.7 27.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 223 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
219A THR* 3.6 9.9 - - + -
220A LEU 3.4 4.0 - - - -
221A PHE* 3.4 39.1 - - + -
81B ILE* 3.7 10.8 - - + +
82B PRO 3.1 22.4 + - - +
83B ASN* 3.1 43.9 + - - +
84B LYS* 4.4 7.4 + - - +
85B GLN 5.5 0.3 + - - -
221B PHE 3.4 1.4 + - - -
222B VAL* 1.3 73.2 - - - +
224B LYS* 1.3 69.6 + - - +
225B GLU* 4.6 2.9 - - - +
231B HIS* 3.6 22.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 224 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
200A GLU* 2.8 42.1 + - - +
204A LYS* 4.3 8.7 - - - +
219A THR* 3.9 3.1 - - - -
220A LEU* 2.8 48.7 + - + +
222A VAL* 5.3 2.2 - - + -
222B VAL* 4.1 22.9 - - + +
223B GLU* 1.3 81.2 - - - +
225B GLU* 1.3 68.2 + - - +
226B LEU* 3.4 3.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 225 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204A LYS* 5.8 0.9 - - - -
219A THR* 4.0 7.6 - - - +
83B ASN* 3.4 25.2 + - - +
85B GLN* 3.1 52.2 + - - +
86B ASP* 4.6 4.3 - - - +
223B GLU* 4.4 3.4 - - - +
224B LYS* 1.3 79.4 - - - +
226B LEU* 1.3 64.6 + - - +
227B GLU 4.0 0.7 + - - -
230B HIS* 3.6 24.8 + - + -
231B HIS* 3.1 42.2 + - + +
----------------------------------------------------------
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