Contacts of the strand formed by residues 177 - 186 (chain B) in PDB entry 3NCF
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 177 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
150B PRO* 3.3 23.7 - - - +
151B GLU* 4.1 10.6 + - - +
175B GLY 4.0 0.6 + - - -
176B GLN* 1.3 80.7 + - - +
178B TYR* 1.3 68.6 + - - +
179B LEU* 4.9 5.2 - - + +
199B PHE* 3.8 33.9 - - + -
200B ILE 3.3 12.8 - - - +
201B GLN* 3.9 34.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 178 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148B LEU* 3.8 27.8 - - + -
149B LYS* 3.4 19.1 - - - -
150B PRO* 3.7 16.8 - - + -
157B GLU* 5.0 7.8 + - - -
172B LEU* 3.6 20.8 - - + +
173B HIS* 2.9 45.0 + + - +
176B GLN* 3.8 20.0 - - + -
177B LYS* 1.3 77.1 - - - +
179B LEU* 1.3 66.1 + - - +
180B VAL* 4.7 0.2 - - + -
198B THR 3.8 0.3 - - - +
199B PHE* 3.3 6.4 - - - +
200B ILE* 2.8 43.9 + - + +
202B ILE* 3.7 33.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 179 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148B LEU* 3.0 26.5 - - - +
149B LYS* 2.7 20.4 + - + +
151B GLU* 4.4 32.5 - - + +
156B TRP* 3.8 25.3 - - + -
177B LYS* 4.9 6.7 - - - +
178B TYR* 1.3 76.7 - - - +
180B VAL* 1.3 60.3 + - - +
181B GLN* 5.6 0.4 - - + -
197B ALA* 4.3 13.2 - - + -
198B THR 3.6 3.8 - - - -
199B PHE* 3.4 38.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 180 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109B LEU* 3.5 13.4 - - + +
111B VAL* 4.3 17.7 - - + -
123B LEU* 4.8 4.5 - - + -
125B ILE* 4.4 18.8 - - + -
146B ILE* 4.1 15.3 - - + -
147B ARG 3.3 8.7 - - - +
148B LEU* 3.9 20.2 - - + -
178B TYR* 4.7 0.7 - - + +
179B LEU* 1.3 80.3 - - - +
181B GLN* 1.3 72.6 + - - +
197B ALA* 3.2 5.9 - - - -
198B THR* 2.9 37.3 + - - +
200B ILE* 4.4 15.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 181 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109B LEU* 4.0 4.0 - - - -
146B ILE* 3.4 7.4 - - - +
147B ARG* 2.7 69.8 + - + +
156B TRP* 3.7 14.1 - - + -
179B LEU* 6.3 0.4 - - - -
180B VAL* 1.3 81.3 - - - +
182B VAL* 1.3 62.5 + - - +
194B TRP* 3.7 24.0 + - + +
195B SER* 2.8 32.1 + - - +
196B PRO* 4.5 0.8 - - - +
197B ALA* 4.0 17.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 182 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106B PRO* 3.6 28.4 - - + +
109B LEU* 4.3 24.5 - - + -
127B TRP* 4.0 31.9 - - + +
144B TYR* 4.5 1.6 - - + -
145B GLU 3.2 19.1 - - - +
146B ILE* 4.3 6.3 - - + -
181B GLN* 1.3 76.8 - - - +
183B ARG* 1.3 65.2 + - - +
194B TRP* 3.6 3.1 - - - -
195B SER* 2.8 43.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 183 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106B PRO* 3.7 7.2 - - - -
144B TYR* 3.4 7.6 - - - +
145B GLU* 2.7 59.3 + - + +
182B VAL* 1.3 75.6 - - - +
184B CYS* 1.3 63.6 + - - +
191B TRP* 3.6 50.1 - - + +
192B SER* 3.5 22.2 + - - +
193B ALA 3.6 9.2 - - - +
194B TRP* 3.3 46.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 184 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103B PRO* 3.8 14.5 - - - +
104B ASP 3.5 24.5 - - - -
106B PRO* 3.8 14.4 - - - -
130B PRO* 4.3 7.0 - - - -
142B LEU* 4.0 13.9 - - + -
143B LEU 3.0 12.1 - - - +
144B TYR* 3.6 17.9 - - + -
183B ARG* 1.3 79.3 - - - +
185B LYS* 1.3 56.8 + - - +
191B TRP* 3.3 7.2 - - - -
192B SER* 2.7 40.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 185 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103B PRO* 4.3 0.2 - - - -
142B LEU* 3.4 7.7 - - - +
143B LEU* 2.8 51.2 + - + +
160B PHE* 5.8 0.7 - - + -
184B CYS* 1.3 74.6 - - - +
186B PRO* 1.3 90.7 + - + +
187B ASP* 3.7 12.9 + - - +
189B GLY 3.7 20.7 + - - +
190B TYR 4.0 0.7 - - - -
191B TRP* 3.4 55.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 186 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17B LYS* 6.0 1.3 - - - -
101B VAL* 3.7 24.7 - - + +
103B PRO* 3.7 9.4 - - + -
140B PHE* 3.7 21.8 - - + -
141B THR 3.3 8.1 - - - +
142B LEU* 4.1 0.4 - - - -
143B LEU* 4.6 2.3 - - - +
185B LYS* 1.3 118.5 + - + +
187B ASP* 1.3 66.7 + - - +
188B ALA 3.4 19.9 + - - +
189B GLY 4.0 8.3 - - - -
190B TYR 3.4 15.0 - - - +
----------------------------------------------------------
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