Contacts of the strand formed by residues 79 - 87 (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 THR 79 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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52A VAL* 3.3 23.1 - - + +
75A ILE* 2.6 26.2 + - - +
76A VAL* 3.0 17.6 + - - +
77A ASP 3.5 1.4 + - - +
78A ARG* 1.3 76.6 - - - +
80A THR* 1.3 60.3 + - - +
81A ALA 3.3 28.9 - - - +
82A VAL* 3.7 19.1 - - + -
97A GLY* 4.1 4.0 - - - -
98A SER 3.4 10.5 - - - +
101A TYR* 2.6 19.4 + - - +
301A MPD 3.9 1.7 + - - +
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Residues in contact with THR 80 (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 PRO* 3.8 3.8 - - - +
52A VAL* 2.9 23.6 + - - +
53A ALA 4.4 1.7 + - - -
78A ARG 5.4 1.3 - - - +
79A THR* 1.3 74.9 - - - +
81A ALA* 1.3 56.8 + - - +
98A SER* 2.7 24.4 + - - +
99A GLY* 4.1 7.1 - - - -
181A GLU* 2.8 29.8 + - - +
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Residues in contact with ALA 81 (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* 3.8 29.4 - - + +
50A PHE 3.5 6.3 - - - +
51A PRO* 4.6 0.9 - - + -
52A VAL* 4.3 0.4 - - - -
79A THR* 3.3 5.9 - - - +
80A THR* 1.3 85.1 + - - +
82A VAL* 1.3 65.0 + - - +
83A TYR* 4.1 8.8 - - + -
96A PHE 3.9 0.7 - - - +
97A GLY* 3.3 1.2 - - - -
98A SER* 3.0 27.3 + - - -
181A GLU* 4.0 23.3 - - + +
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Residues in contact with VAL 82 (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 4.0 0.2 - - - +
49A TYR* 3.4 6.3 - - - -
50A PHE* 2.9 53.8 + - + +
52A VAL* 4.2 11.4 - - + -
59A ILE* 5.5 4.9 - - + -
76A VAL* 5.4 2.2 - - + -
79A THR* 3.7 17.7 - - + -
81A ALA* 1.3 77.1 - - - +
83A TYR* 1.3 72.2 + - - +
84A GLY 4.9 0.2 - - - +
95A LEU* 4.1 19.1 - - + -
96A PHE 3.4 5.6 - - - +
97A GLY* 4.9 0.2 - - - -
301A MPD 3.8 33.7 - - + +
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Residues in contact with TYR 83 (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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36A PRO* 3.5 45.7 - - + +
37A LEU* 4.2 17.7 - - + -
40A VAL* 3.7 6.2 - - + +
48A LEU 3.5 4.7 - - - +
49A TYR* 3.5 27.9 - + + -
81A ALA* 4.1 12.6 - - + -
82A VAL* 1.3 75.5 - - - +
84A GLY* 1.3 58.0 + - - +
95A LEU* 3.2 4.7 - - - +
96A PHE* 2.8 49.4 + + + +
98A SER* 3.9 15.3 + - - -
178A CYS* 3.0 41.7 + - + -
181A GLU* 3.5 16.1 + - - -
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Residues in contact with GLY 84 (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* 5.3 1.3 - - - +
40A VAL* 4.3 5.0 - - - +
47A TYR* 3.4 8.7 - - - +
48A LEU* 2.8 46.2 + - - +
50A PHE* 6.0 0.2 - - - -
82A VAL* 4.2 0.8 - - - +
83A TYR* 1.3 76.0 - - - +
85A ALA* 1.3 61.3 + - - +
94A ARG 3.3 7.9 - - - -
95A LEU* 3.7 13.5 - - - -
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Residues in contact with ALA 85 (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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40A VAL* 3.8 23.8 - - + +
44A ALA* 3.6 20.9 - - + -
46A VAL 3.3 6.7 - - - -
47A TYR* 3.8 5.8 - - + -
48A LEU* 4.1 2.4 - - - +
84A GLY* 1.3 75.2 - - - +
86A PHE* 1.3 58.9 + - - +
87A PHE* 3.7 16.5 - - + -
92A GLU 3.9 0.5 - - - +
93A PHE* 3.3 4.6 - - - +
94A ARG 2.8 32.9 + - - +
95A LEU* 4.9 0.6 - - - +
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Residues in contact with PHE 86 (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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44A ALA* 3.6 1.4 - - - +
45A ASP* 2.9 29.3 + - + -
46A VAL* 2.9 30.6 + - + -
48A LEU* 4.3 1.2 - - + +
85A ALA* 1.3 73.4 - - - +
87A PHE* 1.3 68.1 + - - +
88A ALA* 3.6 33.9 - - + -
91A LYS* 4.5 7.0 - - + -
92A GLU 3.3 22.0 - - - -
93A PHE* 3.8 34.8 - + + -
280A LEU* 3.1 55.2 - - + -
281A TYR* 4.3 6.5 - - + -
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Residues in contact with PHE 87 (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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40A VAL 3.8 6.1 - - - -
41A GLY 4.1 3.1 - - - -
42A SER 3.4 25.4 - - - -
43A GLY 3.7 7.0 - - - -
44A ALA* 3.5 26.5 - - + -
45A ASP* 3.6 3.6 - - - +
85A ALA* 3.7 24.9 - - + -
86A PHE* 1.3 76.0 - - - +
88A ALA* 1.3 60.2 + - - +
89A ARG* 3.4 1.6 - - + +
90A SER* 3.4 17.9 - - - +
91A LYS* 2.9 22.3 + - - -
92A GLU* 2.9 24.4 + - + -
94A ARG* 3.2 54.1 - - + -
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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