Contacts of the strand formed by residues 164 - 169 (chain C) in PDB entry 4BPW
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 164 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110C ILE 3.2 13.5 - - - -
132C TRP* 4.3 7.0 - - - -
135C MET* 3.8 9.6 - - - -
159C TYR* 3.3 12.3 - - - -
160C SER* 2.9 31.4 + - - -
162C ARG 3.6 1.8 + - - -
163C ARG* 1.3 81.0 - - - +
165C VAL* 1.3 64.0 + - - -
1411C MG 4.1 1.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 165 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108C PHE 4.0 0.7 - - - +
110C ILE* 3.1 41.4 + - + +
132C TRP* 4.1 18.6 - - + -
135C MET* 4.5 10.5 - - + +
139C ILE* 3.8 16.8 - - + -
157C TRP* 3.7 29.6 - - + -
158C VAL 3.2 9.4 - - - +
159C TYR* 4.3 1.1 - - - -
160C SER 4.1 0.9 - - - +
164C GLY* 1.3 79.5 - - - +
166C HIS* 1.3 66.2 + - - +
334C ILE* 3.6 26.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 166 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108C PHE 3.3 7.2 - - - +
109C ASP* 3.0 22.6 + - + -
156C LEU 4.5 0.2 - - - -
157C TRP* 3.4 10.1 - - - -
158C VAL* 2.6 42.4 + - + +
159C TYR 5.5 0.2 + - - -
160C SER* 3.2 21.8 - - - -
165C VAL* 1.3 80.8 - - - +
167C CYS* 1.3 60.1 + - - +
168C TRP* 4.2 16.1 + - - +
317C LEU* 4.1 18.4 - - + +
318C LYS* 3.7 41.3 + - + +
331C SER* 5.5 1.4 + - - -
1412C UTP 2.7 27.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 167 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106C LEU 3.5 1.4 - - - +
107C VAL* 3.2 11.1 - - - +
108C PHE* 3.0 38.6 + - + -
146C LEU* 4.1 9.0 - - - -
155C ARG* 4.4 5.4 - - - -
156C LEU 3.4 7.6 - - - -
157C TRP* 3.6 46.6 - - + -
166C HIS* 1.3 75.0 - - - +
168C TRP* 1.3 68.3 + - - +
169C VAL* 4.0 21.8 - - - -
317C LEU* 5.0 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 168 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29C TRP* 3.8 23.8 - + + -
80C ILE* 3.8 32.8 - - + -
104C LYS* 4.6 5.2 - - + -
105C GLU* 4.0 21.1 - - + -
106C LEU 3.8 2.5 - - - -
107C VAL* 3.7 20.0 - - + -
155C ARG* 3.6 1.4 - - - -
156C LEU* 2.7 49.2 + - + +
158C VAL* 3.9 16.4 - - + +
166C HIS* 4.2 8.5 + - + +
167C CYS* 1.3 78.1 - - - +
169C VAL* 1.3 62.1 + - - +
170C CYS* 3.7 17.9 - - - -
317C LEU* 3.6 33.4 - - + +
318C LYS 3.4 23.4 + - - -
320C PRO* 3.9 23.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 169 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105C GLU* 3.4 5.9 - - - +
106C LEU* 2.8 41.3 + - + +
108C PHE* 4.3 7.0 - - + -
146C LEU* 3.8 30.1 - - + -
152C PHE* 3.6 35.7 - - + -
154C HIS 3.4 8.5 - - - +
155C ARG* 4.3 4.9 - - + -
167C CYS* 4.0 7.9 - - - -
168C TRP* 1.3 72.5 - - - +
170C CYS* 1.3 60.9 + - - +
171C ASP* 4.0 2.0 - - - +
174C VAL* 3.4 29.4 - - + +
175C ARG* 4.5 0.2 - - - +
----------------------------------------------------------
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