Contacts of the strand formed by residues 195 - 200 (chain M) in PDB entry 5C7X
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 ILE 195 (chain M).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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154M TRP* 3.4 5.9 - - - -
155M ASN* 2.7 47.6 + - - +
193M THR* 3.9 22.9 - - + -
194M TYR* 1.3 77.4 - - - +
196M CYS* 1.3 69.0 + - - +
197M ASN* 3.5 8.0 + - - +
208M ASP* 3.7 22.7 - - + -
209M LYS 3.3 13.9 - - - +
210M LYS* 3.9 15.9 - - + +
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Residues in contact with CYS 196 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121M VAL* 4.2 8.5 - - - -
140M CYS* 2.0 50.7 - - + -
152M VAL* 4.1 5.2 - - + -
153M SER 3.2 11.0 - - - +
154M TRP* 3.7 21.5 - - + -
195M ILE* 1.3 73.0 - - - +
197M ASN* 1.3 61.2 + - - +
198M VAL* 4.2 15.0 - - - -
207M VAL 3.7 0.9 - - - +
208M ASP* 3.3 5.7 - - - -
209M LYS* 3.2 33.1 + - - -
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Residues in contact with ASN 197 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151M THR 3.1 13.3 - - - +
152M VAL* 4.2 0.7 - - - -
153M SER* 2.6 50.5 + - - +
154M TRP 3.5 0.2 + - - -
156M SER* 2.9 37.4 + - - +
195M ILE* 3.5 18.0 + - - +
196M CYS* 1.3 78.4 + - - +
198M VAL* 1.3 63.4 + - - +
199M ASN* 3.7 0.9 + - - +
206M LYS* 4.2 16.1 - - - +
207M VAL 3.7 0.2 - - - -
208M ASP* 3.4 25.7 + - - +
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Residues in contact with VAL 198 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119M PRO* 4.5 10.1 - - + -
121M VAL* 3.7 39.5 - - + -
140M CYS* 5.0 1.1 - - + -
142M VAL* 3.7 36.3 - - + -
150M VAL* 4.7 8.1 - - + -
151M THR 3.5 4.9 - - - +
152M VAL* 4.3 10.5 - - + +
196M CYS* 4.2 11.9 - - - -
197M ASN* 1.3 72.3 - - - +
199M ASN* 1.3 67.1 + - - +
205M THR* 6.4 0.4 - - + -
206M LYS* 3.3 7.0 - - - +
207M VAL* 2.9 37.1 + - + +
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Residues in contact with ASN 199 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149M PRO 4.5 0.3 - - - +
150M VAL* 3.5 4.2 - - - -
151M THR* 3.0 44.3 + - - +
197M ASN 4.9 0.9 - - - +
198M VAL* 1.3 76.0 - - - +
200M HIS* 1.3 65.3 + - - +
201M LYS* 3.1 39.0 + - - +
204M ASN 5.2 1.0 - - - -
205M THR 2.9 27.5 + - - +
206M LYS* 3.6 28.3 - - + +
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Residues in contact with HIS 200 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116M THR* 4.2 0.7 - - + -
117M LYS 3.4 22.9 + - - -
119M PRO* 3.9 23.8 - - + +
145M TYR* 3.7 7.9 - + - -
146M PHE 3.6 11.3 + - - -
147M PRO 3.0 21.7 + - - -
149M PRO 3.5 11.4 - - - -
150M VAL* 3.4 29.8 - - + -
198M VAL* 4.3 1.4 - - - +
199M ASN* 1.3 70.8 - - - +
201M LYS* 1.3 61.7 + - - +
202M PRO* 3.7 10.8 - - + +
203M SER* 2.7 37.3 + - - +
204M ASN 3.4 2.9 + - - -
205M THR 2.7 30.4 + - - +
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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
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Atomic class I II III IV V VI VII VIII
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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