Contacts of the helix formed by residues 190 - 197 (chain F) in PDB entry 6GL7
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 LEU 190 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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38F GLU* 3.6 26.5 - - - +
164F GLU 3.1 27.8 - - - +
165F LEU 4.0 7.8 + - - +
166F CYS 3.7 9.2 - - - +
167F PHE 3.4 18.4 - - - +
168F PRO* 4.1 27.1 - - + -
169F GLU 5.6 0.7 - - - +
188F PHE 4.3 6.7 - - - +
189F ARG* 1.3 78.6 - - - +
191F LEU* 1.3 65.8 + - - +
192F PRO* 3.5 2.0 - - + -
193F VAL* 3.1 18.5 + - + +
194F GLN 3.1 16.8 + - - -
204F TYR* 4.0 1.0 + - - -
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Residues in contact with LEU 191 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49F PRO* 3.1 37.9 - - + +
50F LEU 3.5 7.8 + - - +
51F LEU* 3.5 29.6 - - - +
52F TYR* 3.6 40.6 - - + +
94F LEU* 3.8 12.6 - - + -
189F ARG* 3.5 6.1 + - + +
190F LEU* 1.3 72.1 - - - +
192F PRO* 1.3 60.9 - - - +
193F VAL 3.2 0.2 + - - -
194F GLN* 3.2 13.6 + - + +
195F PHE* 2.7 32.1 + - - +
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Residues in contact with PRO 192 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38F GLU* 3.4 31.2 - - + +
39F LYS 5.2 4.5 - - - +
44F GLN* 5.3 5.2 - - - +
48F THR* 4.5 12.3 - - + -
49F PRO 3.4 10.3 - - - +
50F LEU* 3.2 22.7 - - + +
154F PHE* 4.5 9.6 - - + -
190F LEU* 3.5 4.5 - - + -
191F LEU* 1.3 90.1 - - + +
193F VAL* 1.3 59.9 + - + +
195F PHE* 4.2 5.2 - - + -
196F LEU* 2.8 41.2 + - + +
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Residues in contact with VAL 193 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154F PHE* 5.6 2.7 - - + -
160F LEU* 5.4 4.7 - - + -
164F GLU 3.9 13.0 - - - +
165F LEU* 3.7 46.2 - - + +
189F ARG* 4.1 16.2 - - - +
190F LEU* 3.1 27.5 + - + +
191F LEU 3.1 0.8 - - - -
192F PRO* 1.3 78.8 - - + +
194F GLN* 1.3 59.6 + - - +
197F CYS* 2.6 48.6 + - + +
200F ILE* 5.2 1.3 - - + +
202F VAL* 5.0 3.6 - - + -
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Residues in contact with GLN 194 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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189F ARG* 2.7 50.5 + - + +
190F LEU 3.1 11.8 + - - +
191F LEU* 3.8 16.2 - - + +
193F VAL* 1.3 75.8 - - - +
195F PHE* 1.3 62.9 + - - +
198F PRO* 3.2 42.1 + - - +
221F LEU* 4.9 4.5 - - + +
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Residues in contact with PHE 195 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45F ALA* 4.0 14.4 - - + -
46F ALA 4.5 5.8 - - - -
47F GLY 4.6 2.0 - - - -
48F THR* 3.2 38.6 - - + -
49F PRO* 3.4 30.1 - - + -
191F LEU 2.7 21.0 + - - +
192F PRO* 4.1 4.7 - - + +
194F GLN* 1.3 74.3 - - - +
196F LEU* 1.3 80.9 + - + +
198F PRO* 3.3 13.5 - - - +
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Residues in contact with LEU 196 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44F GLN* 4.2 17.7 - - + +
45F ALA* 5.0 9.9 - - + +
48F THR* 4.6 6.3 - - + +
154F PHE* 3.4 54.1 - - + -
157F CYS* 3.4 11.3 - - - -
192F PRO* 2.8 23.9 + - + +
195F PHE* 1.3 99.5 - - + +
197F CYS* 1.3 57.4 + - - +
198F PRO* 3.1 9.7 - - - +
199F ASN* 4.7 1.2 - - - +
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Residues in contact with CYS 197 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154F PHE* 3.7 11.4 - - - -
157F CYS* 2.2 48.9 - - + -
160F LEU* 3.7 22.7 - - - -
189F ARG* 4.3 1.2 + - - -
193F VAL* 2.6 35.9 + - + +
196F LEU* 1.3 74.7 - - - +
198F PRO* 1.3 63.5 - - - +
199F ASN* 3.1 6.7 - - - -
200F ILE* 3.0 27.5 + - + +
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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