Contacts of the strand formed by residues 252 - 256 (chain A) in PDB entry 1K3X
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 ARG 252 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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70A LEU* 4.4 2.4 - - - +
158A LEU* 4.1 27.0 - - + +
168A ASN* 3.8 9.6 - - - +
171A ARG* 3.7 9.9 - - - +
248A THR* 3.2 6.9 - - - -
249A LEU 2.8 26.6 + - - +
250A SER 3.1 11.8 - - - +
251A SER* 1.3 88.3 - - - +
253A PRO* 1.3 74.6 - - + +
427C PED 2.9 33.1 + - - -
428C G 2.8 67.6 + - - +
429C A 5.4 6.8 + - - +
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Residues in contact with PRO 253 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168A ASN* 2.9 20.7 + - - +
171A ARG* 3.4 5.7 + - - -
231A HIS* 6.0 1.3 - - - +
246A LYS* 4.6 8.5 - - - -
247A THR 3.5 9.2 - - - +
248A THR* 4.4 3.6 - - + -
252A ARG* 1.3 91.3 - - + +
254A PHE* 1.3 62.5 + - - +
255A TYR* 4.2 17.9 - - + +
426C A 3.8 38.8 - - - +
427C PED 3.4 37.0 - - - +
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Residues in contact with PHE 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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171A ARG* 3.9 11.9 - - - -
172A VAL* 3.6 28.0 - - + -
175A LEU* 4.1 26.0 - - + -
181A THR* 5.3 3.8 - - - -
182A GLY 4.5 8.5 - - - -
245A GLU 3.7 0.5 - - - +
246A LYS* 3.3 5.2 - - - +
247A THR* 2.9 42.5 + - + +
248A THR 4.1 1.6 - - - -
249A LEU* 3.6 51.6 - - + +
253A PRO* 1.3 78.6 - - - +
255A TYR* 1.3 70.4 + - - +
256A TRP* 3.6 35.4 - + + -
261A GLN* 4.7 7.4 - - - -
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Residues in contact with TYR 255 (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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172A VAL* 3.8 15.9 - - + +
229A VAL* 3.3 36.4 - - + +
230A PHE* 3.8 19.1 - + - +
231A HIS* 3.3 51.7 + + - -
232A ARG 4.1 1.1 - - - -
233A ASP* 3.3 29.9 + - - -
244A ILE* 4.6 0.7 - - + -
245A GLU 3.3 6.3 - - - +
246A LYS* 3.5 40.4 - - + +
253A PRO* 4.2 20.0 - - + +
254A PHE* 1.3 84.6 - - - +
256A TRP* 1.3 64.0 + - - +
261A GLN* 4.6 0.9 + - - +
426C A 4.9 2.4 + - - -
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Residues in contact with TRP 256 (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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181A THR* 4.2 15.3 - - + -
229A VAL* 4.6 4.7 - - - -
244A ILE* 3.6 7.4 - - - +
245A GLU* 2.9 70.3 + - + +
247A THR* 3.8 19.4 - - + +
254A PHE* 3.6 28.9 - + + -
255A TYR* 1.3 78.6 - - - +
257A CYS* 1.3 74.1 + - - +
258A PRO* 3.5 28.6 - - + +
261A GLN* 3.2 36.3 - - + +
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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