Contacts of the helix formed by residues 6188 - 6205 (chain F) in PDB entry 2H7C
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 ASN6188 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6176F GLY 4.1 3.2 + - - -
6177F PHE* 4.1 16.7 + - - +
6187F GLY* 1.3 72.9 - - - +
6189F TRP* 1.3 64.8 + - - +
6190F GLY 3.2 3.1 - - - -
6191F HIS* 3.0 6.7 + - + -
6192F LEU* 3.0 22.4 + - + +
6320F GLY 4.2 1.4 + - - +
6321F THR* 3.3 12.7 - - - +
6322F VAL* 2.7 48.9 + - - +
6324F ASP* 3.0 31.2 + - - +
6327F LEU* 3.9 26.9 - - + +
6328F LEU 4.9 0.2 - - - +
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Residues in contact with TRP6189 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6065F PHE* 3.1 44.0 - + - +
6066F THR* 3.6 14.6 - - - -
6067F PRO* 3.7 26.5 - - + -
6171F ARG* 3.8 19.5 + - - +
6175F TRP 3.5 17.5 - - - +
6176F GLY 2.9 17.9 + - - +
6177F PHE 4.2 0.9 - - - -
6178F PHE 3.2 22.2 + - - -
6185F SER* 3.7 13.7 - - - -
6186F ARG* 3.7 16.2 - - + -
6187F GLY* 3.2 32.0 - - - -
6188F ASN* 1.3 72.6 - - - +
6190F GLY* 1.3 57.8 + - - +
6192F LEU* 3.2 16.8 + - + +
6193F ASP* 2.9 34.9 + - - +
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Residues in contact with GLY6190 (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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6170F TYR* 3.3 10.8 - - - +
6171F ARG 3.5 25.1 - - - -
6176F GLY* 2.9 10.9 + - - -
6177F PHE* 3.8 10.1 - - - -
6188F ASN 3.2 0.2 - - - -
6189F TRP* 1.3 78.3 - - - +
6191F HIS* 1.3 60.0 + - - +
6193F ASP* 3.2 12.3 + - - +
6194F GLN* 3.1 20.9 + - - +
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Residues in contact with HIS6191 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6144F LEU* 4.5 2.0 - - + -
6177F PHE* 3.7 27.2 - + - -
6188F ASN* 3.0 15.2 + - - +
6190F GLY* 1.3 73.7 - - - +
6192F LEU* 1.3 66.6 + - - +
6194F GLN* 3.0 29.9 + - - +
6195F VAL* 3.0 25.6 + - - +
6225F GLU* 3.6 10.3 - - - -
6226F SER* 3.4 26.3 + - - -
6229F VAL* 4.4 8.5 - - + +
6230F LEU* 4.5 2.3 - - + +
6321F THR* 2.6 32.3 + - + +
6327F LEU* 3.4 38.6 - - + -
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Residues in contact with LEU6192 (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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6067F PRO* 4.0 22.9 - - + -
6068F PRO* 3.5 16.7 - - + +
6187F GLY 4.6 3.6 - - - +
6188F ASN* 3.0 17.0 + - + +
6189F TRP* 3.2 35.6 + - + +
6191F HIS* 1.3 76.2 - - - +
6193F ASP* 1.3 56.5 + - - +
6195F VAL* 3.3 8.9 + - + +
6196F ALA* 3.0 27.4 + - - +
6235F LEU* 3.7 30.3 - - + -
6324F ASP* 5.3 3.6 - - - +
6326F MET* 5.6 4.7 - - + -
6327F LEU* 4.4 16.2 - - + +
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Residues in contact with ASP6193 (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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6055F PHE* 3.2 16.8 - - + -
6068F PRO* 3.4 16.7 - - - +
6117F LEU* 3.4 17.9 - - + +
6170F TYR* 3.8 11.7 - - + -
6171F ARG* 2.8 65.7 + - - +
6189F TRP 2.9 13.8 + - - +
6190F GLY 3.3 8.3 - - - +
6191F HIS 3.1 0.2 - - - -
6192F LEU* 1.3 75.8 - - - +
6194F GLN* 1.3 60.1 + - - +
6196F ALA* 3.3 1.6 + - - -
6197F ALA* 3.0 23.0 + - - +
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Residues in contact with GLN6194 (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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6139F ILE* 3.6 12.7 - - + +
6168F ILE* 4.1 23.4 - - + +
6170F TYR* 3.5 38.0 - - + -
6190F GLY 3.1 12.2 + - - +
6191F HIS* 3.0 31.4 + - - +
6193F ASP* 1.3 76.8 - - - +
6195F VAL* 1.3 62.4 + - - +
6197F ALA* 3.3 3.5 + - - +
6198F LEU* 3.1 28.2 + - - +
6226F SER* 3.0 32.5 + - - -
6230F LEU* 4.2 19.6 - - + +
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Residues in contact with VAL6195 (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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6191F HIS 3.0 15.3 + - - +
6192F LEU* 3.6 12.3 - - + +
6193F ASP 3.2 0.2 - - - -
6194F GLN* 1.3 76.8 - - - +
6196F ALA* 1.3 57.9 + - - +
6198F LEU* 3.0 10.7 + - - +
6199F ARG* 2.8 28.1 + - + +
6230F LEU* 3.5 24.0 - - + -
6235F LEU* 3.7 21.3 - - + +
6236F ALA* 4.6 5.4 - - + -
6239F LEU* 3.6 21.2 - - + +
6327F LEU* 4.4 11.2 - - + -
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Residues in contact with ALA6196 (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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6055F PHE* 3.9 19.5 - - + +
6056F ALA* 5.0 0.9 - - + -
6068F PRO* 3.7 22.7 - - + +
6192F LEU 3.0 13.9 + - - +
6193F ASP 3.3 8.9 + - - +
6195F VAL* 1.3 79.1 - - - +
6197F ALA* 1.3 56.3 + - - +
6199F ARG* 3.3 9.4 + - - +
6200F TRP* 3.0 27.4 + - - +
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Residues in contact with ALA6197 (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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6055F PHE* 3.7 26.0 - - + -
6119F LEU* 4.5 2.6 - - + +
6168F ILE* 3.9 34.3 - - + -
6193F ASP 3.0 13.8 + - - +
6194F GLN 3.5 8.5 - - - +
6196F ALA* 1.3 75.8 - - - +
6198F LEU* 1.3 59.6 + - + +
6200F TRP* 3.1 5.7 + - - +
6201F VAL* 3.0 31.4 + - - +
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Residues in contact with LEU6198 (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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6137F VAL* 4.0 29.4 - - + -
6139F ILE* 5.9 1.3 - - + -
6168F ILE* 5.7 2.5 - - + -
6194F GLN* 3.1 17.6 + - + +
6195F VAL* 3.0 11.1 + - - +
6197F ALA* 1.3 73.4 - - - +
6199F ARG* 1.3 66.3 + - - +
6201F VAL* 3.2 6.0 + - + +
6202F GLN* 3.0 26.7 + - - +
6215F VAL* 4.5 2.9 - - + -
6217F ILE* 3.6 34.1 - - + -
6230F LEU* 4.1 22.7 - - + -
6236F ALA* 5.2 0.9 - - + -
6239F LEU* 3.9 35.2 - - + +
6240F PHE* 4.4 7.6 - - + -
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Residues in contact with ARG6199 (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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6195F VAL* 2.8 15.2 + - + +
6196F ALA* 3.4 13.7 - - - +
6197F ALA 3.2 0.2 - - - -
6198F LEU* 1.3 75.6 - - - +
6200F TRP* 1.3 64.0 + - - +
6202F GLN* 3.2 34.2 + - - +
6203F ASP* 3.1 48.4 + - - +
6237F LYS 5.9 0.6 + - - -
6238F ASN* 4.9 4.9 + - - +
6239F LEU* 3.8 21.8 - - + +
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Residues in contact with TRP6200 (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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6028F THR* 4.4 12.0 + - + -
6030F HIS* 5.0 17.7 + + - +
6053F ILE* 3.5 26.2 - - + +
6054F PRO 3.9 10.3 + - - -
6055F PHE* 3.8 32.5 - - + +
6074F TRP* 5.9 2.6 - + - -
6119F LEU* 3.8 19.1 - - + -
6121F ILE* 3.8 23.3 - - + -
6196F ALA 3.0 13.4 + - - +
6197F ALA 3.1 8.5 + - - +
6199F ARG* 1.3 78.6 - - - +
6201F VAL* 1.3 69.0 + - + +
6203F ASP* 3.3 1.9 + - - -
6204F ASN* 2.9 72.6 + - + +
6205F ILE* 4.8 5.4 - - + -
6208F PHE* 3.8 19.5 - + - -
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Residues in contact with VAL6201 (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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6119F LEU* 4.8 2.0 - - + -
6135F VAL* 4.3 8.5 - - + -
6137F VAL* 4.3 17.7 - - + -
6166F VAL* 4.5 18.2 - - + -
6168F ILE* 5.7 0.2 - - + -
6197F ALA* 3.0 20.5 + - + +
6198F LEU* 3.5 10.8 - - + +
6199F ARG 3.2 0.2 - - - -
6200F TRP* 1.3 88.0 - - + +
6202F GLN* 1.3 67.0 + - - +
6205F ILE* 2.9 55.0 + - + +
6215F VAL* 4.2 24.5 - - + -
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Residues in contact with GLN6202 (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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6198F LEU 3.0 16.7 + - - +
6199F ARG* 3.2 36.2 + - - +
6201F VAL* 1.3 79.5 - - - +
6203F ASP* 1.3 60.4 + - - +
6204F ASN 3.7 0.2 + - - -
6205F ILE 4.8 0.5 + - - -
6206F ALA* 5.6 0.9 + - - +
6212F PRO* 2.7 50.8 + - - +
6215F VAL* 3.4 21.0 - - - +
6238F ASN 3.8 13.7 - - - +
6239F LEU* 3.6 21.9 + - + -
6241F HIS* 4.2 4.9 + - - -
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Residues in contact with ASP6203 (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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6029F VAL* 3.5 18.8 - - + +
6199F ARG* 3.1 44.3 + - - +
6200F TRP* 3.3 1.3 + - - -
6202F GLN* 1.3 79.8 - - - +
6204F ASN* 1.3 72.9 + - - +
6206F ALA* 5.6 0.4 - - - -
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Residues in contact with ASN6204 (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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6028F THR* 3.4 10.7 - - - +
6029F VAL* 2.9 38.5 + - - +
6030F HIS* 4.6 2.1 + - - -
6200F TRP* 2.9 69.3 + - + +
6203F ASP* 1.3 92.1 - - - +
6205F ILE* 1.3 66.8 + - - +
6206F ALA* 3.2 3.8 - - - -
6207F SER* 3.1 19.9 + - - -
6208F PHE* 3.5 11.9 - - + -
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Residues in contact with ILE6205 (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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6121F ILE* 4.4 17.5 - - + -
6135F VAL* 3.7 21.1 - - + -
6164F VAL* 4.0 11.9 - - + -
6166F VAL* 3.9 26.0 - - + -
6200F TRP* 4.8 4.7 - - + -
6201F VAL* 2.9 35.2 + - + +
6202F GLN 4.8 0.2 + - - -
6204F ASN* 1.3 77.6 - - - +
6206F ALA* 1.3 66.1 + - - +
6208F PHE* 2.9 19.4 + - + -
6210F GLY* 3.0 24.6 + - - +
6211F ASN 4.1 1.1 - - - -
6212F PRO* 3.7 31.9 - - + -
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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