Contacts of the strand formed by residues 189 - 194 (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 THR 189 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149H TRP* 3.5 5.5 - - - -
150H ASN* 2.7 41.8 + - - -
187H THR* 3.3 18.4 - - - +
188H VAL* 1.3 77.9 + - - +
190H CYS* 1.3 65.3 + - - +
191H ASN* 3.8 15.2 + - - +
202H ASP* 3.8 10.1 - - + -
203H LYS 3.5 28.9 - - - +
204H LYS* 3.4 10.1 - - + +
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Residues in contact with CYS 190 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121H VAL* 4.1 0.9 - - - -
122H TYR 5.3 0.4 - - - -
134H GLY 4.3 0.4 - - - -
135H CYS* 2.0 48.9 - - + -
147H VAL* 4.5 4.3 - - + -
148H THR 3.2 9.2 - - - +
149H TRP* 3.6 27.7 - - + -
189H THR* 1.3 72.3 - - - +
191H ASN* 1.3 62.2 + - - +
192H VAL* 3.9 0.7 + - - +
201H VAL 3.6 1.7 - - - +
202H ASP* 3.4 1.9 - - - -
203H LYS* 2.9 54.0 + - - +
205H ILE* 4.3 3.8 - - - -
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Residues in contact with ASN 191 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146H THR 3.1 6.1 - - - +
147H VAL* 3.2 1.9 - - - -
148H THR* 2.7 54.3 + - - +
150H ASN* 3.6 1.6 + - - +
151H SER* 2.7 40.3 + - - +
189H THR* 3.8 16.1 + - - +
190H CYS* 1.3 77.3 - - - +
192H VAL* 1.3 63.1 + - - +
193H ALA* 5.7 0.2 - - - -
201H VAL 3.4 4.3 - - - +
202H ASP* 3.1 25.8 + - - +
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Residues in contact with VAL 192 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119H PRO* 4.2 11.0 - - + -
121H VAL* 3.7 45.1 - - + -
135H CYS* 4.0 10.1 - - - -
137H VAL* 3.9 33.7 - - + -
145H VAL* 4.5 10.1 - - + -
146H THR 3.3 4.9 - - - +
147H VAL* 4.2 8.3 - - + -
190H CYS* 4.7 0.2 - - - -
191H ASN* 1.3 77.7 - - - +
193H ALA* 1.3 65.7 + - - +
194H HIS 4.3 0.2 + - - -
200H LYS* 3.2 2.9 - - - +
201H VAL* 2.8 42.4 + - + +
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Residues in contact with ALA 193 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145H VAL* 3.2 5.5 - - - -
146H THR* 2.8 52.1 + - + +
191H ASN 5.7 0.2 - - - -
192H VAL* 1.3 79.3 - - - +
194H HIS* 1.3 60.6 + - - +
195H PRO* 3.5 10.9 - - + +
199H THR 3.4 7.2 - - - +
200H LYS* 4.4 15.0 - - + -
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Residues in contact with HIS 194 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117H THR 3.2 15.1 + - - -
118H PRO* 4.0 0.8 - - - +
119H PRO* 3.6 16.6 - - + -
140H TYR* 4.1 2.7 - + - -
141H PHE 3.1 27.7 + - - -
142H PRO 2.8 26.8 + - - -
144H PRO 3.6 7.4 - - - -
145H VAL* 3.5 23.6 - - + -
192H VAL* 4.3 0.6 - - - +
193H ALA* 1.3 73.3 - - - +
195H PRO* 1.3 67.1 - - - +
196H ALA* 3.5 17.9 - - + +
197H SER* 2.6 26.9 + - - -
198H SER 3.1 2.8 + - - -
199H THR* 2.8 40.8 + - - +
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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