Contacts of the strand formed by residues 47 - 54 (chain A) in PDB entry 2XKL
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 TRP 47 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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34A MET* 4.5 12.1 - - + -
38A GLU* 6.1 2.2 - - + -
42A PRO* 3.0 38.6 + - + -
45A GLY 4.5 3.8 - - - -
46A LEU* 1.3 75.8 - - - +
48A TYR* 1.3 66.5 + - - +
70A VAL* 3.6 4.9 - - - +
71A PHE* 2.7 59.8 + + + -
73A MET* 3.7 30.2 - - + +
132A GLY 3.5 22.4 - - - -
133A GLY 4.7 1.3 - - - -
134A ILE* 3.6 31.0 - - + -
149A TYR* 4.0 11.4 - - + -
150A ASN 3.7 22.4 - - - -
151A ARG* 3.4 37.7 - - + +
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Residues in contact with TYR 48 (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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46A LEU* 3.9 24.7 - - + +
47A TRP* 1.3 76.8 - - - +
49A PHE* 1.3 61.1 + - - +
50A ILE* 3.6 7.1 + - + +
68A ASN* 5.5 4.7 - - + -
69A ILE 3.3 15.9 - - - +
70A VAL* 3.7 25.5 - - + +
71A PHE* 3.9 4.7 - - - -
149A TYR* 3.1 7.6 - - - +
150A ASN 2.8 38.1 + - - +
151A ARG 3.2 28.0 - - - -
152A SER 4.1 1.6 - - - +
153A PRO* 3.6 47.4 - - + +
180A ARG* 5.8 1.8 - - - -
184A ALA* 4.4 15.7 - - + +
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Residues in contact with PHE 49 (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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48A TYR* 1.3 69.9 - - - +
50A ILE* 1.3 64.5 + - - +
51A ALA* 3.3 32.5 - - - -
52A GLY* 4.3 2.2 - - - -
63A PHE* 3.7 40.6 - + + -
66A VAL* 5.0 0.2 - - + -
68A ASN* 5.7 0.2 - - - +
69A ILE* 3.2 46.3 + - + -
71A PHE* 3.8 9.0 - - + -
147A LEU* 4.0 12.6 - - + -
148A LEU 3.8 3.4 - - - -
149A TYR* 3.8 18.8 - + - -
176A LEU* 4.8 2.7 - - + -
178A THR* 2.9 47.3 + - + +
180A ARG* 4.1 4.5 - - - +
1191A POL 3.7 19.3 - - + -
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Residues in contact with ILE 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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48A TYR* 3.9 12.6 - - + +
49A PHE* 1.3 80.2 - - - +
51A ALA* 1.3 61.2 + - - +
148A LEU* 2.8 30.6 + - + +
149A TYR 4.0 1.3 - - - -
150A ASN* 3.8 20.4 - - + +
152A SER 4.0 7.9 - - - +
153A PRO 4.0 12.1 - - - +
155A PRO* 3.7 30.7 - - + -
159A CYS* 6.1 0.2 - - - -
160A VAL* 3.4 30.7 - - + -
177A VAL* 3.6 4.5 - - - +
178A THR* 3.0 27.6 + - - -
180A ARG* 3.9 16.2 - - - +
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Residues in contact with ALA 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 PHE* 3.3 18.2 - - - -
50A ILE* 1.3 84.2 - - + +
52A GLY* 1.3 58.9 + - - +
147A LEU* 3.7 0.2 - - - -
148A LEU* 2.8 35.8 + - + +
160A VAL* 4.7 1.6 - - + -
163A PHE* 3.9 20.6 - - + -
175A PHE* 4.1 11.9 - - + -
176A LEU 3.1 14.4 - - - +
177A VAL* 4.0 7.9 - - + +
178A THR 4.6 0.7 - - - +
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Residues in contact with GLY 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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49A PHE* 4.3 8.3 - - - -
51A ALA* 1.3 75.3 - - - +
53A ALA* 1.3 62.1 + - - +
60A LEU* 3.6 18.8 - - - +
146A PHE 3.2 9.6 - - - -
147A LEU* 4.7 2.2 - - - -
163A PHE* 4.0 3.1 - - - -
175A PHE* 3.5 5.9 - - - -
176A LEU* 2.8 33.4 + - - +
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Residues in contact with ALA 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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52A GLY* 1.3 75.7 - - - +
54A ALA* 1.3 61.7 + - - +
60A LEU* 4.0 1.5 - - - +
145A ARG* 3.3 3.3 - - - +
146A PHE* 2.7 43.4 + - + -
163A PHE* 4.0 5.6 - - + -
167A THR* 3.4 41.7 - - + +
172A PHE* 4.1 4.0 - - + +
174A ALA 3.3 10.1 - - - +
175A PHE* 3.9 8.7 - - + -
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Residues in contact with ALA 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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53A ALA* 1.3 76.9 - - - +
55A SER* 1.3 62.8 + - - +
56A THR 3.7 8.1 - - - +
59A GLU* 3.5 31.6 - - + +
60A LEU* 3.8 13.9 - - + +
144A GLN 3.8 10.3 - - - +
145A ARG* 4.2 1.3 - - + +
172A PHE* 3.3 17.7 - - - +
174A ALA* 2.9 28.7 + - - +
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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