Contacts of the strand formed by residues 201 - 206 (chain I) in PDB entry 1CL7
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 THR 201 (chain I).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161I TRP* 3.5 9.9 - - - -
162I ASN* 3.1 35.4 + - - +
199I THR* 4.9 3.3 - - - +
200I VAL* 1.3 80.8 + - - +
202I CYS* 1.3 65.9 + - - +
203I ASN* 3.3 10.8 - - - +
214I ASP* 4.0 16.8 - - + +
215I LYS* 3.4 27.6 - - - +
216I LYS* 3.5 13.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 202 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121H VAL* 4.3 1.1 - - - -
123H PRO* 6.2 0.2 - - + -
147I CYS* 2.0 53.2 - - + -
159I VAL* 3.9 8.5 - - - -
160I THR 3.8 3.8 - - - -
161I TRP* 3.9 14.8 - - + -
201I THR* 1.3 72.5 - - - +
203I ASN* 1.3 61.3 + - - +
204I VAL* 3.6 15.7 - - - -
214I ASP* 2.8 8.0 - - - +
215I LYS* 2.6 44.3 + - + +
217I ILE* 4.1 4.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 203 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158I THR 2.8 5.4 - - - +
160I THR* 2.7 77.2 + - + +
161I TRP* 3.2 0.2 - - - -
162I ASN 3.1 18.0 + - - -
163I SER* 3.3 17.2 + - - +
201I THR* 3.3 10.7 + - - +
202I CYS* 1.3 75.2 - - - +
204I VAL* 1.3 61.3 + - - +
213I VAL 3.9 0.2 - - - -
214I ASP* 3.5 26.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 204 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119H PRO* 4.2 13.0 - - + -
121H VAL* 3.7 30.7 - - + -
149I VAL* 3.6 38.1 - - + -
157I VAL* 4.9 3.1 - - + -
158I THR 3.0 5.2 - - - +
159I VAL* 4.2 8.7 - - + -
202I CYS* 3.6 26.0 - - - -
203I ASN* 1.3 72.4 - - - +
205I ALA* 1.3 60.6 + - - +
206I HIS* 4.2 0.8 + - + +
211I THR* 4.3 0.7 - - - +
212I LYS* 3.9 1.3 - - - -
213I VAL* 3.0 35.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 205 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157I VAL* 2.9 7.5 - - - -
158I THR* 2.7 55.5 + - - +
204I VAL* 1.3 73.4 - - - +
206I HIS* 1.3 59.5 + - - +
207I PRO* 3.2 9.6 - - + +
211I THR 3.8 4.7 - - - -
212I LYS* 3.7 27.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 206 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117H THR 3.7 2.8 + - - -
118H PRO* 3.8 0.9 - - + -
119H PRO* 3.4 27.8 - - + -
152I TYR* 3.5 5.8 - + - -
153I PHE 3.1 21.9 + - - -
154I PRO* 2.9 40.4 - - + +
155I GLU* 4.2 1.3 - - - -
156I PRO 2.9 20.3 + - - -
157I VAL* 3.2 15.2 - - + +
204I VAL* 4.2 0.8 + - + -
205I ALA* 1.3 73.7 - - - +
207I PRO* 1.3 65.0 - - - -
208I ALA* 3.0 9.2 + - + +
209I SER* 2.7 41.2 + - - -
210I SER* 3.2 7.7 + - - -
211I THR* 3.0 20.5 + - + +
212I LYS* 5.5 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