Contacts of the helix formed by residues 244 - 254 (chain A) in PDB entry 3KXK
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 ILE 244 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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87A ILE* 3.8 22.9 - - + +
90A LEU* 3.6 44.6 - - + -
91A LEU* 3.5 34.1 - - + -
94A PHE* 3.9 9.5 - - + -
110A ALA* 4.2 5.8 - - + -
240A ILE* 3.6 8.5 - - + -
241A PRO* 3.0 23.5 + - + +
243A GLN* 1.3 85.3 - - + +
245A VAL* 1.3 63.9 + - - +
246A ASP 3.4 2.5 - - - -
247A ALA* 3.4 7.7 + - + +
248A PHE* 3.1 21.7 + - - +
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Residues in contact with VAL 245 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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240A ILE* 4.0 18.6 - - + +
241A PRO 3.5 5.6 + - - +
242A PRO* 3.5 33.4 + - + +
243A GLN 3.5 0.4 - - - -
244A ILE* 1.3 77.6 - - - +
246A ASP* 1.3 66.8 + - - +
248A PHE* 3.3 6.8 + - + +
249A PHE* 2.9 33.0 + - + +
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Residues in contact with ASP 246 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106A GLN* 4.0 21.0 + - - +
242A PRO 5.0 0.2 + - - -
243A GLN 5.2 1.7 + - - +
244A ILE 3.4 0.4 - - - -
245A VAL* 1.3 85.5 - - - +
247A ALA* 1.3 63.7 + - - +
249A PHE* 3.8 5.9 - - - +
250A VAL* 3.2 31.7 + - + +
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Residues in contact with ALA 247 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91A LEU* 4.2 14.8 - - + -
94A PHE* 4.4 3.4 - - + -
103A ALA* 5.2 0.2 - - - +
106A GLN* 3.9 18.2 + - - +
107A ILE* 4.0 32.4 - - + +
110A ALA* 4.6 2.7 - - + -
244A ILE* 3.4 12.8 + - - +
245A VAL 3.3 0.2 - - - -
246A ASP* 1.3 80.2 - - - +
248A PHE* 1.3 59.9 + - - +
250A VAL* 3.6 1.9 + - - +
251A THR* 2.8 29.8 + - - -
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Residues in contact with PHE 248 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94A PHE* 3.4 35.6 - + + -
234A VAL* 4.0 12.8 - - + -
235A PRO 3.5 19.3 - - - -
236A PHE* 4.3 0.7 - - - -
237A ILE* 3.7 28.7 - - + -
240A ILE* 3.3 26.5 - - + -
244A ILE 3.1 17.2 + - - +
245A VAL* 3.7 6.5 - - + +
247A ALA* 1.3 75.0 - - - +
249A PHE* 1.3 65.8 + + + +
251A THR* 3.1 4.5 + - - -
252A LEU* 2.9 56.5 + - + +
284A ILE* 6.1 0.9 - - + -
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Residues in contact with PHE 249 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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245A VAL* 2.9 21.5 + - + +
246A ASP* 3.8 6.7 - - - +
248A PHE* 1.3 84.2 - + + +
250A VAL* 1.3 61.7 + - + +
252A LEU* 3.7 5.3 - - + +
253A SER* 2.7 54.3 + - - -
287A GLU* 3.7 37.7 - - + -
288A ILE* 4.2 11.8 - - + +
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Residues in contact with VAL 250 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100A SER* 4.5 2.9 - - - +
102A GLU* 3.8 31.0 - - + +
103A ALA* 3.7 32.3 - - + +
106A GLN* 4.0 15.5 - - + +
246A ASP* 3.2 19.8 + - + +
247A ALA 4.0 3.1 - - - +
249A PHE* 1.3 83.5 - - + +
251A THR* 1.3 63.4 + - - +
253A SER* 3.3 16.3 + - - -
254A GLU* 3.4 14.2 + - - +
120B LYS* 4.8 3.6 - - - +
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Residues in contact with THR 251 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94A PHE* 3.8 28.2 - - + +
97A HIS* 4.2 2.9 - - + -
98A ALA* 4.0 15.0 - - - +
103A ALA* 3.8 11.3 - - - +
107A ILE* 3.7 19.8 - - - +
233A THR* 6.1 0.3 - - - -
234A VAL* 3.9 23.9 - - + +
247A ALA 2.8 20.4 + - - -
248A PHE* 3.1 7.9 + - - -
250A VAL* 1.3 78.2 - - - +
252A LEU* 1.3 62.1 + - - +
254A GLU* 3.3 21.8 - - - +
255A ALA 4.7 0.2 + - - -
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Residues in contact with LEU 252 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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185A VAL* 5.2 1.1 - - + -
233A THR* 4.9 6.1 - - - +
234A VAL* 3.4 35.2 - - + +
236A PHE* 3.7 34.5 - - + -
248A PHE* 2.9 40.6 + - + +
249A PHE* 3.7 5.4 - - + +
251A THR* 1.3 72.0 - - - +
253A SER* 1.3 62.6 + - - +
254A GLU 3.0 4.9 - - - -
255A ALA* 3.0 26.7 + - + +
284A ILE* 3.8 17.0 - - + -
288A ILE* 3.8 19.9 - - + +
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Residues in contact with SER 253 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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249A PHE* 2.7 48.4 + - - -
250A VAL* 3.3 10.7 + - - -
252A LEU* 1.3 71.6 - - - +
254A GLU* 1.3 61.6 + - - +
255A ALA 3.0 6.1 - - - -
256A LYS* 2.9 49.6 + - - +
257A TYR* 4.1 1.7 - - - -
288A ILE* 4.0 17.6 + - - +
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Residues in contact with GLU 254 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97A HIS 3.9 5.2 - - - +
98A ALA* 3.6 6.5 - - - -
99A GLY* 3.0 24.3 + - - -
100A SER* 2.6 42.1 + - - +
103A ALA* 3.3 12.1 - - - +
218A ARG* 4.6 3.5 + - - -
250A VAL* 3.4 9.6 + - + +
251A THR 3.3 17.7 - - - +
252A LEU 3.0 1.0 - - - -
253A SER* 1.3 77.1 - - - +
255A ALA* 1.3 60.3 + - - +
256A LYS 3.1 1.8 + - - -
257A TYR* 3.2 34.3 + - + +
258A SER* 4.3 2.4 + - - -
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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