Contacts of the strand formed by residues 198 - 203 (chain H) in PDB entry 2CK0
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 198 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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158H TRP* 3.2 14.0 - - - -
159H ASN* 2.8 37.2 + - - -
196H THR* 3.6 16.5 - - - +
197H VAL* 1.3 77.9 + - - +
199H CYS* 1.3 74.7 + - - +
200H ASN* 3.9 10.5 - - - +
211H ASP* 3.7 31.4 - - + -
212H LYS 3.6 6.5 - - - +
213H LYS* 3.9 7.9 - - + +
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Residues in contact with CYS 199 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125H VAL* 4.1 1.6 - - - -
144H CYS* 2.0 53.6 - - + -
156H VAL* 4.7 8.5 - - - -
157H THR 3.9 3.1 - - - -
158H TRP* 3.9 15.0 - - + -
198H THR* 1.3 71.2 - - - +
200H ASN* 1.3 59.1 + - - +
201H VAL* 3.6 19.5 - - - -
210H VAL 3.2 3.1 - - - +
211H ASP* 3.4 1.0 - - - -
212H LYS* 2.7 48.2 + - + +
214H ILE* 4.3 1.6 - - + -
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Residues in contact with ASN 200 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155H THR 3.6 1.3 - - - +
156H VAL* 3.4 4.9 - - - +
157H THR* 2.8 52.2 + - - +
159H ASN* 3.0 13.9 + - - -
160H SER* 2.8 43.3 + - - +
198H THR* 3.5 11.1 - - - +
199H CYS* 1.3 73.2 - - - +
201H VAL* 1.3 62.7 + - - +
209H LYS* 3.5 14.1 - - - +
210H VAL 3.5 4.5 - - - -
211H ASP* 2.9 25.3 + - - -
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Residues in contact with VAL 201 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123H PRO* 4.6 9.2 - - + -
125H VAL* 3.9 24.7 - - + -
146H VAL* 3.9 29.6 - - + -
154H VAL* 3.9 23.1 - - + -
155H THR 3.4 3.4 - - - -
156H VAL* 4.2 4.9 - - + -
199H CYS* 3.6 24.2 - - - -
200H ASN* 1.3 79.6 - - - +
202H ALA* 1.3 65.9 + - - +
208H THR* 4.4 1.0 - - + -
209H LYS* 3.1 9.0 - - - +
210H VAL* 2.9 37.2 + - + +
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Residues in contact with ALA 202 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154H VAL* 3.4 5.0 - - - +
155H THR* 2.8 47.5 + - + +
201H VAL* 1.3 80.1 - - - +
203H HIS* 1.3 61.3 + - - +
204H PRO* 3.5 7.7 - - + +
208H THR 3.2 10.5 - - - +
209H LYS* 4.0 12.3 - - + -
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Residues in contact with HIS 203 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120H THR* 4.0 2.7 - - + -
121H THR 3.6 10.3 - - - -
123H PRO* 3.7 27.3 - - + +
149H TYR* 3.7 8.7 - + + -
150H PHE 3.1 25.5 + - - -
151H PRO 2.8 25.3 + - - -
153H PRO 3.7 5.6 - - - -
154H VAL* 3.3 26.7 - - + -
202H ALA* 1.3 72.1 - - - +
204H PRO* 1.3 70.2 - - - +
205H ALA* 3.6 18.1 - - + +
206H SER* 2.9 31.3 + - - -
208H THR* 3.0 28.3 + - - +
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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) + - + + + + + -
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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