Contacts of the strand formed by residues 183 - 192 (chain A) in PDB entry 4GUP
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 LEU 183 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
181A PRO 4.4 6.1 - - - +
182A PRO* 1.4 74.3 - - - +
184A VAL* 1.4 61.6 + - - +
185A ARG* 4.0 0.3 + - - -
201A LYS 3.5 4.3 - - - +
203A HIS* 2.8 70.9 + - + +
204A GLY* 5.4 4.5 - - - +
183C LEU* 3.7 34.6 - - + +
184C VAL 3.6 24.7 - - - +
185C ARG* 4.2 11.7 - - + -
203C HIS* 4.4 17.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 184 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
182A PRO* 3.8 12.2 + - + -
183A LEU* 1.4 71.9 - - - +
185A ARG* 1.3 66.6 + - - +
186A VAL* 5.1 0.2 - - + -
200A CYS* 3.6 30.7 - - - -
201A LYS 3.3 6.7 - - - +
202A ALA* 3.7 18.4 - - + -
256A CYS* 4.7 0.9 - - - -
258A VAL* 4.0 19.1 - - + -
265A MET* 4.0 19.4 - - - -
267A LEU* 3.8 37.5 - - + +
182C PRO 4.3 10.0 - - - +
183C LEU* 4.4 2.1 - - - +
184C VAL 5.5 2.4 + - - +
265C MET* 4.7 5.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 185 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183A LEU 4.9 0.2 - - - +
184A VAL* 1.3 72.1 - - - +
186A VAL* 1.3 64.2 + - - +
187A ASN* 4.2 14.9 + - - +
199A PHE 3.7 0.5 - - - +
200A CYS* 3.7 0.7 - - - -
201A LYS* 2.8 61.0 + - - +
203A HIS* 4.2 13.1 + - - -
267A LEU* 4.6 3.4 - - - -
14B PRO* 3.7 36.8 - - - +
181C PRO* 3.8 39.5 - - + +
182C PRO 4.4 2.9 - - - +
183C LEU* 3.6 31.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 186 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184A VAL* 5.1 0.2 - - + -
185A ARG* 1.3 79.8 - - - +
187A ASN* 1.3 62.8 + - - +
188A ARG* 6.3 0.2 - - + -
198A LEU* 4.6 4.9 - - + -
199A PHE 3.2 13.5 - - - +
200A CYS* 4.1 16.6 - - + -
214A TRP* 3.5 31.9 - - + -
256A CYS* 4.2 11.9 - - + -
267A LEU* 4.2 21.5 - - + +
268A GLN 6.5 0.7 - - - -
269A VAL* 3.8 18.8 - - + -
181C PRO* 4.7 12.3 - - - +
263C VAL* 5.4 11.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 187 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185A ARG* 4.5 13.5 + - - +
186A VAL* 1.3 77.0 - - - +
188A ARG* 1.3 67.6 + - - +
189A LYS* 3.5 4.5 + - - +
199A PHE* 2.9 41.8 + - - +
201A LYS* 3.7 28.9 - - - +
97B ARG 5.7 0.5 - - - +
181C PRO* 6.0 3.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 188 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186A VAL* 6.3 0.2 - - + -
187A ASN* 1.3 76.1 - - - +
189A LYS* 1.3 61.0 + - - +
196A THR* 5.4 10.3 - - + -
197A ALA 3.5 8.5 - - - +
198A LEU* 3.8 17.4 - - + +
246A LEU* 4.0 23.5 - - + +
269A VAL* 3.5 16.8 - - - +
270A PRO* 3.1 40.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 189 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187A ASN* 3.5 6.2 + - - +
188A ARG* 1.3 75.0 - - - +
190A GLU* 1.3 61.2 + - - +
191A THR* 3.7 4.9 - - + +
196A THR* 3.3 9.2 - - - -
197A ALA 2.8 29.7 + - - +
199A PHE* 3.7 31.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 190 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189A LYS* 1.3 73.6 - - - +
191A THR* 1.4 61.8 + - - +
192A PHE* 3.1 25.9 + - - +
193A PRO* 3.4 14.1 - - - +
194A GLY* 4.0 14.7 - - - -
195A VAL 3.4 12.3 - - - +
196A THR* 3.7 17.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 191 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189A LYS* 3.7 4.1 + - + +
190A GLU* 1.4 72.2 - - - +
192A PHE* 1.3 65.3 + - - +
195A VAL* 3.4 16.7 + - - +
197A ALA* 3.7 29.4 + - + +
199A PHE* 4.1 19.7 - - + -
243A SER* 6.0 0.4 - - - +
245A GLU* 5.3 5.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 192 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
190A GLU* 3.1 7.5 - - - +
191A THR* 1.3 84.1 + - - +
193A PRO* 1.3 90.2 - - + +
195A VAL* 2.5 55.1 + - + +
----------------------------------------------------------
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