Contacts of the strand formed by residues 48 - 54 (chain B) in PDB entry 1KI6
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 THR 48 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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46B MET 4.8 2.0 - - - +
47B PRO* 1.3 75.1 - - - +
49B LEU* 1.3 61.1 + - - +
147B ALA* 3.2 32.8 - - + -
154B PRO 4.1 5.4 + - - -
155B PRO* 3.9 10.0 - - - +
156B ALA* 3.2 27.0 + - - +
157B LEU 3.9 2.4 + - - -
349B GLN* 3.4 21.9 + - - +
350B THR 3.0 4.0 - - - +
351B HIS* 3.6 16.8 - - + +
352B VAL* 5.3 0.2 - - - -
358B ILE* 4.1 4.7 - - - +
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Residues in contact with LEU 49 (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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48B THR* 1.3 75.5 - - - +
50B LEU* 1.3 69.9 + - - +
51B ARG* 4.2 13.2 + - + -
139B LEU* 6.1 0.2 - - + -
143B ILE* 3.8 22.9 - - + -
155B PRO* 4.5 0.9 - - - -
157B LEU* 3.2 46.9 - - + +
159B LEU* 4.5 9.6 - - + +
349B GLN* 3.2 7.8 - - - -
350B THR* 2.4 49.3 + - - +
352B VAL* 4.1 14.6 - - + -
358B ILE* 4.9 1.3 - - + -
361B ILE* 3.8 28.0 - - + -
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Residues in contact with LEU 50 (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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49B LEU* 1.3 75.1 - - - +
51B ARG* 1.3 61.7 + - - +
52B VAL* 3.4 29.8 - - + -
155B PRO* 3.6 25.9 - - + +
157B LEU 3.2 7.6 + - - +
158B THR* 3.4 16.1 - - + +
159B LEU* 2.8 27.5 + - - +
202B ASN* 3.3 29.4 - - - +
344B THR* 4.4 22.2 - - + +
347B MET* 3.8 16.6 - - + +
348B VAL 3.4 10.1 - - - +
349B GLN* 3.9 15.0 - - + +
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Residues in contact with ARG 51 (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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49B LEU* 4.2 13.4 + - + +
50B LEU* 1.3 78.9 - - - +
52B VAL* 1.3 63.1 + - - +
53B TYR* 2.6 50.9 + - + -
139B LEU* 4.5 6.5 - - - -
143B ILE* 4.0 25.2 - - - +
159B LEU* 3.5 10.5 - - + -
161B PHE* 3.9 19.5 - - + -
164B HIS* 5.5 0.4 + - - -
198B LEU* 3.6 26.7 - - - +
199B PRO 2.3 35.6 + - - -
200B GLY* 3.4 18.8 + - - +
201B THR* 3.5 9.5 + - - +
202B ASN* 2.7 36.8 + - - +
348B VAL 4.8 0.4 + - - -
350B THR* 4.8 3.0 + - - +
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Residues in contact with VAL 52 (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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50B LEU* 3.4 27.4 - - + -
51B ARG* 1.3 80.0 - - - +
53B TYR* 1.3 63.2 + - - +
54B ILE* 3.6 20.4 + - + +
158B THR* 4.5 0.7 - - + -
159B LEU 3.0 6.5 + - - +
160B ILE* 3.5 24.2 - - + -
161B PHE* 2.9 26.3 + - - +
202B ASN* 3.6 2.7 - - - +
204B VAL* 3.7 22.7 - - + -
340B LEU* 4.6 5.6 - - + -
344B THR* 4.7 4.9 - - - +
347B MET* 3.8 17.9 - - + -
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Residues in contact with TYR 53 (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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51B ARG* 2.6 49.0 + - + -
52B VAL* 1.3 74.3 - - - +
54B ILE* 1.3 62.2 + - - +
55B ASP 3.5 0.7 + - - -
136B ASP* 4.5 9.0 + - - -
139B LEU* 4.7 4.0 - - - +
161B PHE* 3.7 37.0 - + + -
163B ARG 3.6 21.1 - - - +
164B HIS* 3.2 39.2 + + + -
165B PRO* 4.3 8.3 - - + -
198B LEU* 5.0 0.2 - - - +
201B THR* 3.8 10.5 - - + -
202B ASN 2.9 27.4 + - - +
203B ILE* 3.5 18.0 - - + +
204B VAL* 2.7 28.1 + - - +
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Residues in contact with ILE 54 (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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52B VAL* 3.6 24.2 - - + +
53B TYR* 1.3 70.6 - - - +
55B ASP* 1.3 60.8 + - - +
62B LYS* 3.7 23.5 + - + +
66B THR* 3.4 32.1 - - + -
160B ILE* 3.6 19.5 - - + -
161B PHE 3.2 9.4 + - - +
162B ASP* 4.0 3.0 - - - +
163B ARG* 2.9 25.9 + - - +
204B VAL* 3.7 15.5 - - + +
329B TYR* 3.5 24.7 - - + +
340B LEU* 4.1 17.9 - - + -
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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