Contacts of the strand formed by residues 159 - 167 (chain A) in PDB entry 6D3N
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 GLY 159 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158A SER* 1.3 79.3 + - - +
160A SER* 1.3 63.5 + - - -
184A ASP* 3.5 7.6 - - - +
185A LEU* 3.0 25.3 + - - +
219A GLU 3.5 9.6 - - - -
220A ALA* 4.1 1.1 - - - -
221A ARG 4.7 0.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 160 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159A GLY* 1.3 70.3 - - - -
161A VAL* 1.3 66.5 + - - +
162A SER* 5.1 2.1 + - - -
182A THR* 4.5 11.4 - - - +
183A VAL 3.3 9.9 - - - -
184A ASP* 3.2 27.8 - - - +
185A LEU* 4.2 4.9 - - - +
217A HIS* 5.7 0.2 - - - -
218A THR* 3.5 3.1 + - - -
219A GLU* 2.9 43.2 + - - +
220A ALA* 4.7 0.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 161 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102A LEU* 4.5 11.0 - - + -
147A LEU* 4.6 10.0 - - + +
149A LEU* 4.1 20.2 - - + -
160A SER* 1.3 79.6 - - - +
162A SER* 1.3 65.4 + - - +
181A LEU 4.0 0.2 - - - +
182A THR* 3.5 4.3 - - - +
183A VAL* 2.9 32.7 + - - +
185A LEU* 3.6 31.6 - - + -
216A LEU* 3.6 28.0 - - + -
217A HIS 3.3 12.8 - - - +
218A THR* 4.4 12.1 - - - -
228A LEU* 5.4 0.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 162 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147A LEU* 5.5 0.9 - - - -
160A SER* 5.1 2.4 + - - -
161A VAL* 1.3 75.2 + - - +
163A LEU* 1.3 62.6 - - - +
164A ALA* 6.2 1.1 - - - -
181A LEU 3.3 6.1 - - - -
182A THR* 3.3 22.2 + - - +
215A HIS 3.6 0.7 - - - +
216A LEU* 3.2 9.9 - - - +
217A HIS* 2.6 54.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 163 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107A LEU* 3.8 13.0 - - + -
109A TRP* 5.6 1.1 - - + -
145A PHE* 3.8 37.0 - - + -
146A GLN 4.4 7.2 - - - +
147A LEU* 4.0 37.7 - - + +
162A SER* 1.3 75.6 - - - +
164A ALA* 1.3 60.9 + - - +
180A ALA* 3.3 4.7 - - - +
181A LEU* 2.9 39.3 + - + +
214A VAL* 3.6 18.6 - - + -
215A HIS 3.3 14.1 - - - +
216A LEU* 3.7 18.8 - - + -
233A THR* 4.5 6.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 164 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145A PHE* 4.4 2.9 - - - -
162A SER* 6.2 1.1 - - - -
163A LEU* 1.3 75.5 - - - +
165A LEU* 1.3 61.1 + - - +
166A HIS* 3.7 25.7 + - + +
177A ALA* 4.1 10.3 - - + -
179A LEU 3.4 8.5 - - - +
180A ALA* 4.7 3.6 - - + -
213A GLY 3.7 0.2 - - - +
214A VAL* 3.4 3.3 - - - -
215A HIS* 2.9 38.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 165 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143A VAL* 4.2 16.2 - - + -
145A PHE* 4.1 9.6 - - + -
164A ALA* 1.3 71.6 - - - +
166A HIS* 1.3 61.6 + - - +
167A LEU* 5.0 0.9 - - + -
177A ALA* 3.6 3.6 - - - -
178A ALA* 3.0 31.1 + - + +
179A LEU* 2.8 32.0 + - + -
204A LEU* 4.0 28.0 - - + -
212A LEU* 4.0 35.0 - - + -
213A GLY 3.4 15.3 - - - +
214A VAL* 3.7 19.3 - - + +
235A LEU* 4.4 7.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 166 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164A ALA* 3.7 24.6 - - + +
165A LEU* 1.3 75.7 - - - +
167A LEU* 1.3 64.8 + - - +
168A GLN 3.5 2.0 + - - +
170A LEU* 4.7 18.1 - - + +
175A GLY* 3.6 22.9 + - - -
176A ALA 3.8 13.7 + - - -
177A ALA* 4.2 13.9 - - + -
178A ALA 5.0 0.2 - - - +
212A LEU* 3.7 1.7 - - - -
213A GLY* 2.8 37.1 + - - +
215A HIS* 3.7 33.5 - + + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 167 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165A LEU* 4.3 2.4 + - + -
166A HIS* 1.3 74.1 - - - +
168A GLN* 1.3 69.0 + - - +
169A PRO 3.1 13.9 - - - +
170A LEU* 4.2 7.2 + - - +
176A ALA 5.3 2.8 + - - -
178A ALA* 4.2 24.1 - - + +
204A LEU* 4.8 4.0 - - + -
205A HIS 4.8 5.4 - - - +
206A LEU* 3.6 29.4 - - + -
210A GLN* 4.0 24.2 - - + +
211A ARG 3.8 0.4 - - - -
212A LEU* 3.7 22.7 - - + -
----------------------------------------------------------
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