Contacts of the strand formed by residues 49 - 54 (chain A) 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 LEU 49 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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48A THR* 1.3 74.7 - - - +
50A LEU* 1.3 69.8 + - - +
51A ARG* 4.2 12.9 + - + +
139A LEU* 5.9 0.2 - - + -
143A ILE* 3.9 22.2 - - + -
155A PRO* 4.5 3.1 - - - -
157A LEU* 3.2 48.2 - - + +
159A LEU* 4.3 9.2 - - + +
348A VAL 4.8 0.2 - - - +
349A GLN* 3.5 4.3 - - - -
350A THR* 2.7 39.8 + - - +
351A HIS* 4.8 0.2 - - - +
352A VAL* 4.0 15.0 - - + -
358A ILE* 4.7 0.9 - - + -
361A ILE* 3.5 31.4 - - + -
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Residues in contact with LEU 50 (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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49A LEU* 1.3 75.9 - - - +
51A ARG* 1.3 53.4 + - - +
52A VAL* 3.3 30.7 - - + -
155A PRO* 4.2 11.4 - - + -
157A LEU 2.8 12.2 + - - +
158A THR* 3.2 19.3 - - + +
159A LEU* 2.5 36.0 + - - +
202A ASN* 3.3 30.1 - - - +
344A THR* 4.6 16.4 - - + +
347A MET* 3.9 18.6 - - + +
348A VAL 3.5 14.8 - - - +
349A GLN* 4.1 15.9 - - + +
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Residues in contact with ARG 51 (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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49A LEU* 4.2 9.5 + - + +
50A LEU* 1.3 74.3 - - - +
52A VAL* 1.3 63.5 + - - +
53A TYR* 2.7 48.2 + - + -
136A ASP* 5.1 0.2 + - - -
139A LEU* 4.1 11.2 - - - +
143A ILE* 3.9 22.0 - - - +
159A LEU* 3.2 16.6 - - + -
161A PHE* 3.5 24.2 - - + -
164A HIS* 5.6 0.4 + - - -
198A LEU* 3.6 30.9 - - - +
199A PRO 2.6 30.9 + - - -
200A GLY 3.6 16.1 + - - +
201A THR* 3.8 7.7 + - - -
202A ASN* 2.9 30.9 + - - +
348A VAL 5.0 0.6 + - - -
350A THR* 5.0 3.6 + - - +
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Residues in contact with VAL 52 (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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50A LEU* 3.3 33.2 - - + -
51A ARG* 1.3 74.1 - - - +
53A TYR* 1.3 62.2 + - - +
54A ILE* 3.6 19.9 + - + +
159A LEU 2.7 10.2 + - - +
160A ILE* 3.5 25.2 - - + -
161A PHE* 2.7 28.9 + - - +
202A ASN 3.7 3.1 - - - +
204A VAL* 3.7 23.3 - - + -
340A LEU* 4.6 4.7 - - + -
344A THR* 4.9 3.8 - - - +
347A MET* 3.8 17.0 - - + -
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Residues in contact with TYR 53 (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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51A ARG* 2.7 50.4 + - + -
52A VAL* 1.3 76.3 - - - +
54A ILE* 1.3 63.0 + - - +
55A ASP 3.3 1.3 + - - +
136A ASP* 4.4 9.6 + - + +
139A LEU* 4.4 3.8 - - - +
161A PHE* 3.6 36.4 - + + -
163A ARG 3.6 7.9 - - - -
164A HIS* 3.3 52.5 - + + +
165A PRO* 4.2 6.5 - - + -
201A THR* 4.2 10.8 - - + -
202A ASN 3.0 19.5 + - - +
203A ILE* 3.6 18.1 - - + +
204A VAL 2.8 27.2 + - - -
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Residues in contact with ILE 54 (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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52A VAL* 3.6 26.5 - - + +
53A TYR* 1.3 70.3 - - - +
55A ASP* 1.3 59.3 + - - +
62A LYS* 3.6 24.6 + - + +
66A THR* 3.5 32.3 - - + -
160A ILE* 3.7 17.9 - - + -
161A PHE 3.1 9.1 + - - +
162A ASP* 4.0 2.9 - - - +
163A ARG* 3.0 25.7 + - - +
204A VAL* 3.7 15.7 - - + +
329A TYR* 3.4 25.4 - - + +
340A LEU* 4.2 17.3 - - + -
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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