Contacts of the strand formed by residues 203 - 210 (chain M) in PDB entry 2GTL
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 HIS 203 (chain M).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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49M GLN* 4.3 24.2 + - - -
196M PHE* 3.3 17.6 - - - -
198M LEU* 3.6 33.0 - - + +
200M ASP* 3.1 31.3 + - - +
202M ASP* 1.3 89.4 - - + +
204M ALA* 1.3 60.8 + - - +
221M ASN* 5.6 4.9 - - - +
222M ALA 3.5 7.0 - - - +
223M GLN* 3.9 30.2 + - + -
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Residues in contact with ALA 204 (chain M).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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111M TYR* 5.5 1.7 - - + -
194M CYS* 4.2 0.4 - - + -
195M ASP 3.1 15.9 - - - +
196M PHE* 3.4 31.9 - - + -
198M LEU* 4.6 6.9 - - - +
203M HIS* 1.3 76.9 - - - +
205M ASP* 1.3 57.8 + - - +
206M CYS* 3.5 14.6 - - - -
221M ASN* 3.7 6.5 - - - +
222M ALA* 2.8 41.6 + - + +
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Residues in contact with ASP 205 (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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193M ILE 3.8 2.8 - - - +
195M ASP* 2.8 39.2 + - + +
197M ASN* 5.1 2.9 - - - +
198M LEU* 4.8 14.2 - - + +
204M ALA* 1.3 69.8 - - - +
206M CYS* 1.3 61.7 + - - +
207M LYS* 4.1 17.7 + - - -
219M HIS* 3.3 29.0 + - - -
220M PHE 4.6 1.6 - - - -
221M ASN* 3.9 16.2 + - - +
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Residues in contact with CYS 206 (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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111M TYR* 5.0 1.8 - - - -
130M VAL* 4.5 4.0 - - - -
192M VAL* 4.5 0.7 - - + -
193M ILE 3.2 5.4 - - - -
194M CYS* 2.0 45.8 - - - -
204M ALA* 3.5 6.9 - - - -
205M ASP* 1.3 76.2 - - - +
207M LYS* 1.3 62.5 + - - +
219M HIS* 3.9 5.0 - - - -
220M PHE* 2.8 72.3 + - + +
222M ALA* 4.0 13.5 - - - -
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Residues in contact with LYS 207 (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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192M VAL* 4.4 2.0 - - - -
193M ILE* 2.8 48.4 + - + +
195M ASP* 3.7 24.7 + - - -
205M ASP* 4.1 20.7 + - - +
206M CYS* 1.3 76.2 - - - +
208M ILE* 1.3 64.3 + - - +
209M VAL* 3.3 6.2 - - + +
216M VAL* 3.8 25.6 - - + -
218M ALA 3.4 12.6 - - - +
219M HIS* 4.2 10.8 - - + +
220M PHE 4.6 0.2 - - - +
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Residues in contact with ILE 208 (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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115M ALA* 4.3 18.4 - - + -
117M TRP* 3.8 35.2 - - + -
128M ALA* 4.5 6.1 - - + -
151M LEU* 4.2 16.6 - - + -
153M TYR* 4.6 5.4 - - + -
190M TYR* 3.5 33.7 - - + -
191M GLY 3.5 9.0 - - - +
192M VAL* 4.3 0.9 - - - +
207M LYS* 1.3 69.3 - - - +
209M VAL* 1.3 54.4 + - - +
216M VAL 3.6 1.0 - - - -
217M CYS* 2.7 30.7 + - + +
218M ALA* 2.8 23.1 + - + +
220M PHE* 3.8 22.4 - - + -
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Residues in contact with VAL 209 (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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180M LEU 5.3 0.7 - - - +
190M TYR* 3.2 13.9 - - - +
191M GLY* 2.9 40.0 + - - -
192M VAL 4.0 1.8 - - - +
193M ILE* 3.4 22.0 - - + -
207M LYS* 3.3 18.6 - - + +
208M ILE* 1.3 74.9 - - - +
210M VAL* 1.3 72.2 + - - +
211M PRO* 3.9 2.7 - - + -
214M LEU* 3.8 36.3 - - + +
215M PHE 3.3 12.8 - - - +
216M VAL* 4.6 7.6 - - + -
217M CYS* 4.0 1.3 - - - +
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Residues in contact with VAL 210 (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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14A GLU* 3.1 33.9 - - + +
131A ASN* 5.0 4.0 - - - +
190M TYR* 4.4 6.5 - - + -
209M VAL* 1.3 75.2 - - - +
211M PRO* 1.3 76.1 - - + -
212M SER* 3.0 5.0 + - - +
213M SER* 3.1 13.2 + - - +
214M LEU 2.7 22.7 + - - -
215M PHE* 2.9 36.7 + - + +
217M CYS* 4.2 13.0 - - - -
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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