Contacts of the strand formed by residues 207 - 212 (chain X) in PDB entry 4GL1
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 VAL 207 (chain X).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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27X ARG* 3.0 8.1 + - - +
141X LEU* 3.5 11.7 - - + +
143X VAL* 3.6 28.5 - - + +
195X PRO* 3.7 0.2 - - - +
196X GLY 2.8 36.8 + - - +
197X SER 3.5 23.1 - - - +
198X LEU* 3.6 21.5 - - + +
206X CYS* 1.3 83.1 - - - +
208X THR* 1.3 69.7 + - - +
209X TRP* 3.3 30.5 - - + +
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Residues in contact with THR 208 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27X ARG* 5.2 0.9 + - - +
83X PRO* 4.0 12.6 - - + +
84X LEU* 3.9 27.4 - - + +
88X TYR* 4.7 4.9 + - - -
138X PRO 5.2 1.0 + - - -
139X ASP* 5.0 10.4 - - - +
141X LEU 2.9 14.8 + - - -
142X ALA* 3.3 4.2 - - - +
143X VAL 3.1 22.2 + - - +
193X THR* 3.8 19.3 - - - +
194X TYR 4.0 5.8 - - - +
195X PRO* 4.8 3.4 - - + +
206X CYS 4.1 0.4 + - - -
207X VAL* 1.3 72.5 - - - +
209X TRP* 1.3 61.2 + - - +
210X ILE* 3.8 2.9 + - + +
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Residues in contact with TRP 209 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29X SER* 3.0 20.7 + - - -
107X HIS* 3.5 21.3 - + - -
117X GLU* 4.5 0.4 - - - -
119X HIS* 3.5 39.9 - + - -
143X VAL* 3.4 45.1 - - + -
145X GLY* 4.6 4.3 - - - -
193X THR* 2.8 35.6 + - - -
194X TYR* 3.0 38.1 + + + +
196X GLY* 3.9 7.9 - - - -
197X SER 3.0 28.1 + - - -
198X LEU* 5.3 1.1 - - - -
199X THR* 3.8 16.2 - - + -
207X VAL* 3.3 22.4 - - + +
208X THR* 1.3 72.2 - - - +
210X ILE* 1.3 56.3 + - - +
211X VAL* 4.1 10.1 - - + -
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Residues in contact with ILE 210 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47X LEU* 3.9 17.7 - - + -
79X LEU* 4.2 11.4 - - + -
83X PRO* 3.9 28.5 - - + -
84X LEU* 3.8 32.1 - - + -
142X ALA* 4.8 3.6 - - + -
143X VAL 3.0 10.0 + - - +
144X LEU* 3.3 23.7 - - + +
145X GLY 2.8 23.6 + - - -
191X TYR* 3.7 31.2 - - + -
192X TRP 3.4 3.8 - - - -
193X THR* 4.1 1.3 - - - +
208X THR* 4.3 4.9 - - + +
209X TRP* 1.3 78.0 - - - +
211X VAL* 1.3 59.1 + - - +
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Residues in contact with VAL 211 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33X ILE* 3.9 18.6 - - + -
107X HIS* 4.1 35.9 - - + +
117X GLU* 5.5 0.4 - - - +
145X GLY* 3.4 13.7 - - - +
147X PHE* 3.5 37.0 - - + -
191X TYR* 3.2 2.3 - - - -
192X TRP* 2.8 44.0 + - + +
194X TYR* 4.8 3.1 - - + -
209X TRP* 4.3 13.0 - - + -
210X ILE* 1.3 77.9 - - - +
212X LEU* 1.3 66.3 + - - +
213X LYS 3.6 0.2 + - - -
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Residues in contact with LEU 212 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47X LEU* 4.5 5.4 - - + -
144X LEU* 3.7 28.3 - - + -
145X GLY 2.9 15.9 + - - +
146X ILE* 3.8 16.2 - - + -
147X PHE* 3.8 21.5 + - - -
185X LEU* 5.2 0.9 - - + -
186X PRO* 3.6 33.2 - - + -
188X SER 4.1 2.2 - - - +
189X LEU* 3.8 33.0 - - + +
190X ASP 3.4 12.6 - - - +
191X TYR* 3.9 9.2 - - + -
192X TRP* 4.1 0.8 - - - -
211X VAL* 1.3 74.1 - - - +
213X LYS* 1.3 64.2 + - - +
214X GLU 3.6 13.3 + - - +
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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
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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