Contacts of the helix formed by residues 300 - 311 (chain B) in PDB entry 3KTC
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 ASP 300 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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298B LYS 3.4 4.9 + - - +
299B LEU* 1.3 75.0 - - - +
301B ILE* 1.3 57.4 + - - +
302B PRO* 3.5 11.4 - - - +
303B ALA* 3.1 31.9 + - + +
304B LEU* 2.9 27.7 + - - +
319B ILE* 3.6 12.4 + - + +
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Residues in contact with ILE 301 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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256B TYR* 4.0 19.7 - - + -
259B LYS* 3.6 37.0 - - + -
260B ILE* 4.4 7.2 - - + -
296B LEU 4.6 3.6 - - - +
299B LEU* 3.0 31.5 + - + +
300B ASP* 1.3 71.2 - - - +
302B PRO* 1.3 68.4 - - + +
304B LEU* 3.2 5.1 + - - +
305B GLN* 2.8 56.5 + - - +
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Residues in contact with PRO 302 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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300B ASP* 3.5 10.8 - - - +
301B ILE* 1.3 94.6 - - + +
303B ALA* 1.3 55.8 + - - +
305B GLN* 3.3 7.5 + - + +
306B ALA* 3.0 29.0 + - - +
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Residues in contact with ALA 303 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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300B ASP* 3.1 34.6 + - + +
302B PRO* 1.3 76.3 - - - +
304B LEU* 1.3 61.1 + - - +
306B ALA* 3.3 6.7 + - - +
307B ALA* 3.0 19.1 + - - +
319B ILE* 3.5 24.4 - - + +
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Residues in contact with LEU 304 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136A PHE* 3.8 20.2 - - + +
256B TYR* 3.7 34.3 - - + +
299B LEU* 4.1 13.2 - - + -
300B ASP 2.9 14.1 + - - +
301B ILE* 3.5 7.0 - - - +
303B ALA* 1.3 77.2 - - - +
305B GLN* 1.3 57.5 + - - +
307B ALA* 3.1 4.7 + - - +
308B GLN* 2.9 47.7 + - - +
316B ALA* 3.8 37.5 - - + +
319B ILE* 3.7 12.7 - - + +
320B VAL* 4.0 10.8 - - + -
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Residues in contact with GLN 305 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139A SER* 6.3 0.7 - - - -
256B TYR* 3.0 27.8 + - - +
260B ILE* 3.8 18.0 - - - +
301B ILE* 2.8 36.3 + - - +
302B PRO* 3.9 6.7 - - + +
304B LEU* 1.3 76.3 - - - +
306B ALA* 1.3 56.9 + - - +
308B GLN* 3.3 12.6 + - - +
309B GLU* 2.9 28.9 + - - +
339B EDO 5.2 3.6 + - - -
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Residues in contact with ALA 306 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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302B PRO 3.0 17.9 + - - +
303B ALA* 3.6 8.5 - - - +
305B GLN* 1.3 74.9 - - - +
307B ALA* 1.3 63.6 + - - +
309B GLU* 3.3 8.6 + - - +
310B ALA* 3.1 20.8 + - - +
315B GLN* 5.3 0.4 - - - -
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Residues in contact with ALA 307 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137A GLN 4.7 0.2 - - - -
303B ALA 3.0 14.0 + - - +
304B LEU* 3.1 8.9 + - - +
306B ALA* 1.3 76.1 - - - +
308B GLN* 1.3 58.6 + - - +
310B ALA* 3.1 4.1 + - - -
311B GLN 2.8 21.7 + - - -
312B ASN 2.9 16.0 + - - +
315B GLN* 3.7 28.5 - - + +
316B ALA* 3.7 29.8 - - - +
319B ILE* 4.5 1.1 - - + -
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Residues in contact with GLN 308 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136A PHE* 2.9 39.8 + - - +
137A GLN 3.4 10.3 - - - +
138A VAL* 3.3 19.2 + - - -
139A SER* 3.6 30.7 + - - +
253B GLU* 5.3 0.4 + - - -
256B TYR* 3.8 20.9 + - - -
304B LEU* 2.9 39.1 + - + +
305B GLN* 3.6 13.1 - - - +
306B ALA 3.2 0.2 - - - -
307B ALA* 1.3 75.5 - - - +
309B GLU* 1.3 64.2 + - - +
311B GLN* 3.0 21.7 + - - +
316B ALA* 4.9 0.4 - - + -
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Residues in contact with GLU 309 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96A PRO* 3.6 23.4 - - - +
101A ARG* 5.5 5.0 + - - -
139A SER* 6.0 0.2 - - - -
142A ASN* 4.6 16.1 + - - +
305B GLN 2.9 13.1 + - - +
306B ALA* 3.3 11.4 + - - +
308B GLN* 1.3 76.5 - - - +
310B ALA* 1.3 60.4 + - - +
311B GLN* 3.4 3.3 + - - +
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Residues in contact with ALA 310 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90A ARG* 3.1 18.5 + - - -
96A PRO* 3.8 11.5 - - - +
306B ALA 3.1 12.7 + - - +
307B ALA* 3.1 9.6 + - - +
309B GLU* 1.3 75.2 - - - +
311B GLN* 1.3 64.9 + - - +
312B ASN* 3.2 13.4 + - + +
315B GLN* 4.8 3.4 - - - +
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Residues in contact with GLN 311 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90A ARG* 3.0 23.5 + - - +
94A THR* 2.8 28.5 + - - +
95A ASN 4.1 0.2 - - - -
96A PRO* 3.6 24.0 - - + +
131A GLY 4.2 9.2 - - - +
137A GLN* 3.0 37.0 + - + +
138A VAL* 4.2 16.2 - - + +
143A LEU* 4.2 15.9 - - - +
146A LEU* 4.8 7.1 - - - +
173A ARG* 4.9 5.4 + - - -
307B ALA 2.8 5.7 + - - -
308B GLN 3.0 19.8 + - - +
309B GLU 4.2 2.7 + - - +
310B ALA* 1.3 79.6 - - - +
312B ASN* 1.3 58.6 + - - +
313B PRO* 3.4 1.8 - - - +
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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