Contacts of the strand formed by residues 46 - 51 (chain A) in PDB entry 3K8G
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 VAL 46 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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44A ALA* 3.7 2.8 - - - +
45A ASP* 1.3 86.5 - - + +
47A TYR* 1.3 76.2 + - - +
48A LEU* 3.8 18.1 - - + +
85A ALA* 3.3 4.3 - - - -
86A PHE* 2.9 42.4 + - + -
189A LEU* 4.1 9.2 - - + -
190A TYR 3.3 8.5 - - - +
191A ILE* 4.0 27.1 - - + -
197A PHE* 5.4 0.9 - - + -
280A LEU* 3.9 33.4 - - + -
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Residues in contact with TYR 47 (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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37A LEU* 4.5 10.1 - - + -
40A VAL* 4.3 10.1 - - + -
41A GLY 2.7 29.6 + - - -
42A SER* 3.3 3.1 - - - -
43A GLY 3.2 8.1 + - - -
44A ALA* 3.1 42.6 + - + -
45A ASP 5.5 0.2 - - - -
46A VAL* 1.3 75.7 - - - +
48A LEU* 1.3 63.7 + - - +
84A GLY 3.4 10.8 - - - -
85A ALA* 3.8 8.7 - - + -
168A PRO* 3.7 20.3 - - + +
169A GLN 5.3 2.7 - - - -
170A LEU* 3.8 31.6 - - + -
174A PHE* 3.8 10.5 - - + -
189A LEU* 3.3 4.2 - - - -
190A TYR* 2.8 43.5 + + - +
192A LYS* 4.2 10.8 - - + -
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Residues in contact with LEU 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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37A LEU* 5.2 1.4 - - - +
46A VAL* 3.8 23.8 - - + +
47A TYR* 1.3 81.8 - - - +
49A TYR* 1.3 62.8 + - - +
50A PHE* 3.7 34.5 - - + -
82A VAL 4.5 0.4 - - - -
83A TYR* 3.5 3.5 - - - +
84A GLY* 2.8 51.5 + - - +
85A ALA 4.1 1.3 - - - +
86A PHE 4.3 5.2 - - - +
93A PHE* 4.4 17.7 - - + -
95A LEU* 5.9 1.1 - - + -
174A PHE* 3.9 5.5 - - - -
188A ALA 3.4 7.0 - - - +
189A LEU* 4.1 16.2 - - + -
277A ILE* 4.1 20.4 - - + -
280A LEU* 5.2 1.1 - - + -
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Residues in contact with TYR 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 LEU* 1.3 77.8 - - - +
50A PHE* 1.3 62.8 + - - +
51A PRO* 3.6 29.4 - - + +
81A ALA* 3.8 15.3 - - + +
82A VAL 3.4 7.0 - - - -
83A TYR* 3.5 42.6 - + + -
174A PHE* 4.1 5.4 - - + -
177A GLU* 3.2 40.1 + - + -
178A CYS* 3.8 21.1 + - - -
180A SER* 4.5 0.7 - - - -
181A GLU* 3.7 28.9 + - - +
184A SER 5.3 0.6 + - - -
186A THR 4.0 8.3 - - - -
187A VAL* 3.4 7.6 - - - +
188A ALA* 2.9 36.5 + - + +
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Residues in contact with PHE 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 LEU* 3.7 40.2 - - + -
49A TYR* 1.3 79.0 - - - +
51A PRO* 1.3 67.7 - - + +
52A VAL* 3.4 2.3 + - - +
55A ASN* 5.2 0.4 - - + -
58A LEU* 3.8 20.0 - - + -
59A ILE* 4.1 29.8 - - + -
62A ILE* 4.1 15.7 - - + -
81A ALA* 3.5 0.6 - - - -
82A VAL* 2.9 54.3 + - + +
84A GLY* 6.0 0.4 - - - -
95A LEU* 6.2 2.5 - - + -
187A VAL* 3.7 31.0 - - + -
189A LEU* 5.3 0.2 - - + -
277A ILE* 4.0 15.0 - - + -
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Residues in contact with PRO 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 TYR* 3.6 26.6 - - + +
50A PHE* 1.3 83.4 - - - +
52A VAL* 1.3 61.3 + - - +
53A ALA* 4.4 5.6 - - + +
55A ASN* 2.8 34.2 + - - +
80A THR 3.8 7.9 - - - +
81A ALA* 4.5 1.1 - - + -
181A GLU* 5.6 4.3 - - + -
184A SER 3.8 16.2 - - - +
185A GLN* 3.5 23.3 - - - -
186A THR 3.1 31.6 - - - +
187A VAL* 4.1 0.2 - - - -
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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