Contacts of the strand formed by residues 169 - 176 (chain H) in PDB entry 2FD6
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 169 (chain H).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114H ALA* 4.1 9.6 - - + -
115H LYS 4.7 0.7 - - - +
117H THR* 4.0 19.5 - - + +
139H GLY* 3.6 33.0 - - - +
140H TYR 3.8 3.4 - - - +
141H PHE* 3.6 26.9 - - + -
165H LEU* 3.3 6.2 - - - -
166H GLN 2.7 36.3 + - - +
167H SER* 2.9 11.5 + - - +
168H ASP* 1.3 85.4 - - + +
170H TYR* 1.3 63.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 170 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110H THR* 3.7 24.0 + - + +
139H GLY 2.9 22.6 + - - -
140H TYR* 2.9 58.0 + + + +
141H PHE* 3.4 27.8 - + - -
142H PRO* 4.4 0.4 - - + -
143H GLU* 3.8 35.4 - - + +
163H ALA* 4.0 14.4 - - + -
164H VAL 3.3 17.7 - - - -
165H LEU* 3.4 24.5 - - + +
169H LEU* 1.3 72.7 - - - +
171H THR* 1.3 63.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 171 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136H LEU* 3.7 26.2 - - + -
137H VAL 3.2 6.3 - - - +
138H LYS* 3.8 14.4 - - + +
139H GLY 3.9 1.2 + - - -
162H PRO 4.4 0.5 - - - +
163H ALA* 3.2 2.2 - - - -
164H VAL* 2.8 46.9 + - + +
166H GLN* 2.6 39.8 + - - +
170H TYR* 1.3 79.1 + - - +
172H LEU* 1.3 64.9 + - - +
177L THR* 5.6 7.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 172 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136H LEU* 3.6 5.8 - - - +
137H VAL* 2.7 55.3 + - + +
140H TYR* 3.6 19.3 - - + +
143H GLU* 5.3 1.6 - - - +
145H VAL* 3.5 27.1 - - + +
147H VAL* 3.9 14.8 - - + -
160H THR* 4.2 11.4 - - + -
161H PHE 3.4 20.4 - - - +
162H PRO* 4.9 2.0 - - + -
163H ALA* 4.0 10.8 - - + +
171H THR* 1.3 76.7 - - - +
173H SER* 1.3 76.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 173 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124H LEU* 4.8 2.7 - - - -
135H CYS 3.2 12.3 - - - -
136H LEU* 4.4 13.0 - - - -
161H PHE* 3.0 31.7 + - - +
172H LEU* 1.3 85.0 - - - +
174H SER* 1.3 62.8 + - - +
132L VAL* 5.0 2.7 - - - -
134L PHE* 3.6 15.8 - - - -
175L SER* 3.0 28.3 + - - -
177L THR* 5.2 1.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 174 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134H GLY* 2.5 34.8 - - - -
135H CYS* 2.8 12.1 + - - -
147H VAL* 3.8 21.7 - - - +
149H TRP* 3.1 22.6 + - - -
158H VAL* 3.8 3.3 - - - +
159H HIS 3.1 7.9 + - - -
160H THR* 2.8 27.7 + - - -
161H PHE* 4.5 0.4 - - - -
172H LEU* 5.0 0.2 - - - -
173H SER* 1.3 75.9 - - - +
175H SER* 1.3 54.8 + - - +
134L PHE* 3.6 4.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 175 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132H THR* 3.8 9.4 - - - +
133H LEU 3.1 6.1 - - - -
134H GLY* 3.8 0.2 - - - -
149H TRP* 4.5 1.1 - - - -
157H GLY 3.6 0.6 + - - +
158H VAL* 3.3 6.9 - - - +
159H HIS* 2.8 47.3 + - - +
161H PHE* 4.2 0.5 - - - -
174H SER* 1.3 74.5 - - - +
176H VAL* 1.3 62.0 + - - +
177H THR* 5.2 1.0 + - - -
134L PHE* 3.4 34.9 - - - -
136L ASN* 3.2 19.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 176 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131H VAL 3.7 1.0 - - - +
132H THR* 3.2 5.1 - - - -
133H LEU* 2.7 44.6 + - + +
149H TRP* 3.6 39.0 - - + -
154H LEU* 3.8 28.3 - - + -
156H SER 5.1 1.1 - - - +
157H GLY 3.3 5.8 - - - +
158H VAL* 4.0 17.3 - - + -
175H SER* 1.3 74.7 - - - +
177H THR* 1.3 67.1 + - - +
178H VAL* 4.2 9.2 - - + -
188H VAL* 4.2 6.5 - - + -
----------------------------------------------------------
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