Contacts of the strand formed by residues 169 - 181 (chain D) in PDB entry 5GAG
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 ARG 169 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2773A C 3.2 41.7 + - - +
2774A C 3.5 34.2 + - - +
110D THR* 3.5 24.9 - - + +
111D GLY 3.2 8.3 - - - +
112D THR* 4.6 1.5 - - - +
168D GLU* 1.3 79.0 - - - +
170D VAL* 1.3 67.9 + - - +
202D ILE* 4.2 20.4 - - - +
204D LYS* 4.0 20.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 170 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2678A C 3.9 21.3 - - - +
2679A A 4.0 26.7 - - - +
2773A C 4.7 2.5 - - - -
109D VAL 3.8 1.4 - - - +
110D THR* 3.3 3.5 - - - -
111D GLY 2.9 31.6 + - - +
113D SER* 4.0 10.3 - - - +
168D GLU* 3.7 26.2 - - + +
169D ARG* 1.3 81.8 - - - +
171D THR* 1.3 72.1 + - - +
172D VAL* 4.8 1.8 - - + -
194D PRO* 3.8 17.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 171 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2678A C 5.3 2.1 + - - -
2772A C 3.4 34.6 + - - +
2773A C 2.9 23.9 + - - -
108D ASP* 4.5 8.7 - - + -
109D VAL 3.5 6.5 - - - +
110D THR* 3.2 19.3 + - - +
170D VAL* 1.3 79.9 - - - +
172D VAL* 1.3 79.6 + - - +
173D GLN* 3.9 19.5 + - + +
204D LYS* 4.8 1.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 172 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2678A C 5.5 2.2 - - - +
2679A A 4.1 9.2 - - - +
2729A G 4.5 11.7 - - - +
2730A C 4.0 18.6 - - - +
108D ASP* 3.4 5.4 - - - +
109D VAL 2.9 33.7 + - - +
170D VAL* 4.8 4.5 - - + -
171D THR* 1.3 77.0 - - - +
173D GLN* 1.3 63.3 + - - +
175D LEU* 3.7 30.3 - - + +
192D ALA 4.1 14.8 - - - +
194D PRO* 3.7 29.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 173 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2730A C 2.9 28.0 + - - +
2731A G 4.2 18.5 - - - +
2771A C 3.4 18.8 + - - -
2772A C 3.7 15.3 + - - -
108D ASP* 3.2 11.3 + - - +
171D THR* 3.9 14.6 - - + +
172D VAL* 1.3 82.3 - - - +
174D SER* 1.3 69.8 + - - +
175D LEU* 3.3 4.7 + - - +
207D VAL* 3.3 28.3 - - - +
208D LYS* 3.2 35.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 174 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2730A C 3.6 14.6 - - - +
2731A G 3.3 24.1 + - - -
106D LYS* 4.0 25.8 + - - +
107D VAL 3.9 1.1 - - - -
108D ASP* 2.4 23.3 + - - -
173D GLN* 1.3 72.9 - - - +
175D LEU* 1.3 62.1 + - - +
176D ASP* 4.0 6.1 + - - +
206D ALA* 4.8 2.3 - - - +
208D LYS* 4.8 9.9 + - - +
209D ALA 3.4 21.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 175 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2729A G 3.8 22.4 - - - +
2730A C 4.0 6.7 - - - -
106D LYS* 3.1 7.4 - - - +
107D VAL* 2.9 44.0 + - + +
109D VAL* 3.9 18.2 - - + -
172D VAL* 3.7 29.8 - - + +
173D GLN 3.9 6.5 - - - +
174D SER* 1.3 75.1 - - - +
176D ASP* 1.3 62.3 + - - +
189D VAL* 4.8 4.9 - - + -
190D LYS 3.8 15.9 - - - +
191D GLY* 4.7 0.9 - - - -
192D ALA 4.4 8.3 - - - +
193D VAL* 3.7 29.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 176 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2730A C 4.0 17.3 + - - +
105D LYS* 3.7 15.0 + - - +
106D LYS* 3.7 26.8 + - - +
174D SER 4.1 5.0 - - - +
175D LEU* 1.3 78.4 - - - +
177D VAL* 1.3 63.5 + - - +
178D VAL* 3.4 2.0 + - + -
189D VAL* 3.4 5.9 - - - -
190D LYS* 3.0 50.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 177 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101D PHE* 4.7 2.5 - - + +
104D VAL 3.5 25.1 - - - +
105D LYS* 3.0 13.4 + - - +
107D VAL* 3.7 37.2 - - + -
176D ASP* 1.3 71.2 - - - +
178D VAL* 1.3 62.9 + - - +
179D ARG* 4.1 6.3 - - - +
180D VAL* 3.5 31.4 - - + -
187D LEU* 4.0 16.2 - - + -
188D LEU 4.1 3.1 - - - +
189D VAL* 4.5 2.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 178 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14D ILE* 4.7 14.4 - - + -
22D ILE* 4.3 28.3 - - + -
24D VAL* 4.6 15.3 - - + -
176D ASP* 3.4 3.1 + - + +
177D VAL* 1.3 76.7 - - - +
179D ARG* 1.3 64.7 + - + +
188D LEU* 2.7 21.5 + - + +
190D LYS* 3.6 34.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 179 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14D ILE* 3.7 29.6 - - - +
177D VAL* 4.3 0.7 - - - -
178D VAL* 1.3 86.1 - - + +
180D VAL* 1.3 77.6 + - - +
181D ASP* 4.2 16.8 - - - +
184D ARG* 4.7 6.0 - - - +
186D LEU 3.9 0.5 - - - +
187D LEU* 3.7 4.0 - - - +
188D LEU* 2.9 63.2 + - + +
8Q LEU* 4.0 18.4 - - - +
11Q GLU* 4.4 6.1 + - - -
12Q GLN* 5.6 3.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 180 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98D VAL* 3.9 40.2 - - + +
99D GLU* 4.0 9.9 - - - +
101D PHE 3.7 16.4 - - - +
102D ALA* 4.3 19.7 - - - +
177D VAL* 3.5 23.3 - - + -
179D ARG* 1.3 84.0 - - - +
181D ASP* 1.3 63.2 + - - +
182D ALA 4.2 0.5 + - - -
186D LEU 3.7 2.5 - - - +
187D LEU* 3.9 6.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 181 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98D VAL* 4.0 3.2 - - - +
179D ARG* 4.2 15.6 - - - -
180D VAL* 1.3 74.3 - - - +
182D ALA* 1.3 60.4 + - - +
183D GLU* 3.4 21.0 + - - +
184D ARG* 3.0 43.6 + - + +
185D ASN* 3.0 6.6 + - - -
186D LEU* 2.8 51.2 + - + +
----------------------------------------------------------
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