Contacts of the strand formed by residues 194 - 199 (chain H) in PDB entry 2R4S
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 194 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154H TRP* 3.5 14.7 - - - -
155H ASN* 3.0 46.6 + - - +
156H SER* 4.4 4.7 - - - +
192H THR* 4.5 3.8 + - - +
193H VAL* 1.3 75.6 - - - +
195H CYS* 1.3 71.2 + - - +
196H ASN* 4.4 5.2 - - - +
207H ASP* 4.0 9.7 - - + +
208H LYS 3.4 25.3 + - - -
209H LYS* 3.8 11.6 + - - +
210H ILE* 5.3 0.2 - - - -
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Residues in contact with CYS 195 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121H VAL* 3.4 16.8 - - - -
140H CYS* 2.0 52.9 - - + -
153H THR 3.9 4.9 - - - -
154H TRP* 3.7 21.5 - - + +
194H THR* 1.3 78.4 + - - +
196H ASN* 1.3 60.5 + - - +
197H VAL* 4.2 3.0 - - - +
206H VAL 3.8 0.3 - - - +
207H ASP* 3.5 1.7 - - - -
208H LYS* 2.9 32.1 + - - +
210H ILE* 5.2 1.1 - - + -
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Residues in contact with ASN 196 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152H VAL* 3.6 6.6 - - - +
153H THR* 2.9 45.8 + - + +
154H TRP 3.5 0.5 - - - -
155H ASN* 3.1 10.4 + - - -
156H SER* 2.7 51.1 + - - +
194H THR* 4.3 5.6 - - - +
195H CYS* 1.3 73.2 - - - +
197H VAL* 1.3 73.4 + - - +
205H LYS* 5.1 12.6 - - - +
206H VAL 3.2 7.0 - - - +
207H ASP* 3.0 21.5 + - - +
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Residues in contact with VAL 197 (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 20.0 - - + -
121H VAL* 3.2 46.9 - - + -
140H CYS* 4.5 3.6 - - - -
142H VAL* 4.6 9.6 - - + -
150H VAL* 4.9 4.9 - - + -
151H THR 3.5 9.9 - - - +
152H VAL* 4.2 13.7 - - + -
153H THR* 5.2 0.6 - - - +
195H CYS* 4.2 4.5 - - - -
196H ASN* 1.3 84.3 - - - +
198H ALA* 1.3 66.5 + - - +
205H LYS* 3.3 4.8 - - - +
206H VAL* 2.6 46.3 + - + +
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Residues in contact with ALA 198 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
150H VAL* 3.1 11.0 - - - +
151H THR* 2.7 50.5 + - + +
197H VAL* 1.3 80.7 - - - +
199H HIS* 1.3 62.0 + - - +
200H PRO* 3.3 8.3 - - + +
204H THR 3.4 4.7 - - - +
205H LYS* 4.7 13.7 - - + -
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Residues in contact with HIS 199 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116H THR* 4.0 4.0 - - + -
117H THR 3.8 5.8 - - - -
118H PRO* 3.5 2.6 - - - +
119H PRO* 3.5 32.2 - - + +
145H TYR* 4.1 1.6 - - + -
146H PHE 2.9 35.9 + - - -
147H PRO 3.1 11.9 + - - -
149H PRO 3.6 16.2 - - - -
150H VAL* 4.0 7.9 - - + -
197H VAL* 5.2 0.2 - - - +
198H ALA* 1.3 73.5 - - - +
200H PRO* 1.3 54.9 - - - -
201H ALA* 3.0 29.1 - - + +
202H SER* 2.7 28.6 + - - +
203H SER 2.6 27.4 + - - -
204H THR* 2.7 19.4 + - - +
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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