Contacts of the strand formed by residues 172 - 178 (chain H) in PDB entry 3CII
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 SER 172 (chain H).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151A SER* 4.2 9.5 + - - -
154A GLU* 5.1 4.9 - - - -
155A HIS* 3.2 25.8 + - - -
170H SER* 4.1 5.5 - - - +
171H PRO* 1.3 82.5 - - - +
173H SER* 1.3 63.8 + - - +
210H VAL* 6.2 0.4 - - - -
211H LEU 3.3 6.5 - - - -
212H GLN* 4.4 8.3 - - - -
225H ILE* 4.3 15.3 - - - -
226H ILE* 3.6 28.0 - - - +
228H HIS* 4.2 3.8 + - - -
----------------------------------------------------------
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
----------------------------------------------------------
155H LEU* 3.8 13.3 - - - +
172H SER* 1.3 76.5 - - - +
174H TRP* 1.3 74.3 + - - +
175H ILE 3.6 0.2 + - - -
210H VAL* 3.3 7.6 - - - +
211H LEU* 2.7 46.3 + - - +
225H ILE* 4.6 2.1 - - - +
226H ILE 3.1 9.8 + - - -
228H HIS* 3.2 39.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 174 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138H ARG 3.4 19.4 + - - -
140H TRP* 3.2 38.7 - + + +
143H SER* 3.2 22.2 - - - -
154H LEU* 4.1 18.9 - - + +
155H LEU* 3.9 10.0 - - - +
173H SER* 1.3 83.4 + - - +
175H ILE* 1.3 60.3 + - - +
208H CYS* 3.6 24.9 - - + -
209H ALA 3.2 23.1 - - - -
210H VAL* 3.2 18.4 - - + +
219H ALA* 4.0 7.6 - - + -
220H GLN 3.3 24.2 - - - -
221H CYS* 3.8 7.6 - - - -
223H SER 3.2 22.4 - - - -
225H ILE* 3.5 22.6 - - + +
226H ILE 3.2 15.6 + - - +
227H TYR* 4.9 1.3 - - + -
228H HIS 4.7 0.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 175 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140H TRP* 3.3 14.9 + - - -
154H LEU* 3.8 4.0 - - - -
155H LEU* 3.2 19.7 - - + +
156H SER* 5.3 0.9 - - - -
157H ILE* 4.2 19.3 - - + +
173H SER 3.6 8.0 + - - +
174H TRP* 1.3 79.4 - - - +
176H GLY* 1.3 52.9 + - - +
177H VAL* 2.6 40.6 + - + +
194H PHE* 4.6 1.6 - - + -
209H ALA* 3.4 35.7 + - + +
210H VAL 4.3 0.4 - - - +
211H LEU* 4.2 16.4 - - + -
216H LEU* 3.4 36.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 176 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140H TRP* 4.5 0.7 - - - -
154H LEU* 3.7 16.7 - - - +
155H LEU 2.9 16.6 + - - -
156H SER* 4.9 6.9 - - - +
175H ILE* 1.3 66.6 - - - +
177H VAL* 1.3 65.2 + - - +
188H THR* 3.4 19.9 - - - -
189H MET* 3.5 33.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 177 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140H TRP* 4.6 1.6 + - - -
156H SER* 6.5 0.9 - - - -
157H ILE 6.3 0.7 - - - +
175H ILE* 2.6 29.4 + - + +
176H GLY* 1.3 78.8 - - - +
178H PHE* 1.3 63.7 + - - +
186H TRP* 3.5 27.1 - - + -
187H VAL 3.3 8.7 - - - +
188H THR* 4.6 2.9 - - + -
194H PHE* 3.7 57.2 - - + -
198H ILE* 4.9 1.6 - - + -
208H CYS* 3.8 1.2 - - - +
209H ALA* 3.1 30.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 178 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140H TRP* 3.7 29.4 - + + -
177H VAL* 1.3 75.4 - - - +
179H ARG* 1.3 76.1 + - - +
180H ASN* 3.5 23.1 - - - -
186H TRP* 3.9 7.9 - - - -
187H VAL* 2.9 41.4 + - + +
188H THR 4.2 12.8 - - - -
189H MET* 4.0 25.1 - - + -
207H ASN* 3.2 12.1 - - + +
208H CYS* 4.4 11.7 - - - -
----------------------------------------------------------
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