Contacts of the strand formed by residues 53 - 60 (chain A) in PDB entry 6Q6Q
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 53 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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40A THR* 4.9 1.7 + - - +
50A GLY* 2.9 26.9 + - - -
51A ALA 3.4 2.6 + - - -
52A CYS* 1.3 76.0 - - - +
54A VAL* 1.3 71.1 + - - +
70A PRO* 4.4 5.6 - - + -
71A ALA 3.4 8.5 - - - +
72A ASN* 3.9 1.0 + - - +
89A VAL* 5.3 1.6 - - - +
119A PRO 4.4 2.8 - - - +
120A GLY* 3.7 11.1 - - - -
123A MET* 3.2 35.0 - - + +
124A SER* 3.3 22.9 - - - +
147A ASN* 3.6 11.6 + - - -
348A GLN* 3.7 16.4 - - + +
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Residues in contact with VAL 54 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27A LEU* 4.2 8.1 - - + -
31A LEU* 4.3 3.1 - - + -
40A THR* 4.0 16.6 - - + +
52A CYS 3.8 6.7 - - - +
53A THR* 1.3 79.8 - - - +
55A MET* 1.3 61.8 + - - +
56A ILE* 4.1 20.4 - - + -
70A PRO* 3.3 6.4 - - - +
71A ALA 2.9 41.1 + - - +
73A ALA* 4.0 19.5 - - + +
76A ILE* 4.6 0.7 - - + -
86A VAL* 4.3 4.3 - - + -
87A THR 3.5 10.1 - - - +
88A THR* 3.8 25.4 - - + -
123A MET* 4.2 5.6 - - - -
127A THR* 5.0 0.4 - - - -
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Residues in contact with MET 55 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54A VAL* 1.3 74.7 - - - +
56A ILE* 1.3 68.5 + - - +
57A SER* 3.9 15.5 - - - +
68A HIS* 3.9 21.8 - - + +
69A HIS 3.7 3.4 - - - +
70A PRO* 4.4 0.2 - - - -
85A ALA 3.4 5.2 - - - +
86A VAL* 3.4 2.4 - - - -
87A THR* 2.9 55.8 + - + +
123A MET* 3.8 9.4 - - + +
126A TYR* 3.6 29.8 - - + +
127A THR* 3.6 41.3 - - + +
130A ARG* 4.5 13.9 - - - +
216A LEU* 5.7 1.6 - - + -
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Residues in contact with ILE 56 (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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27A LEU* 4.5 1.1 - - + -
54A VAL* 4.1 15.5 - - + -
55A MET* 1.3 77.4 - - - +
57A SER* 1.3 64.7 + - - +
58A ARG* 4.0 16.4 - - + +
67A ARG 3.7 1.7 - - - +
68A HIS* 3.7 1.0 - - - -
69A HIS* 3.0 51.6 + - + +
71A ALA* 4.0 22.7 - - + -
76A ILE* 4.2 9.6 - - + -
81A LEU* 4.0 16.6 - - + -
84A ALA* 4.0 22.7 - - + -
85A ALA 3.7 1.6 - - - +
86A VAL* 3.8 26.7 - - + -
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Residues in contact with SER 57 (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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55A MET* 3.9 14.7 - - - +
56A ILE* 1.3 75.6 - - - +
58A ARG* 1.3 62.2 + - - +
66A ILE* 4.7 0.2 - - - -
67A ARG 3.5 4.7 - - - -
68A HIS* 2.9 31.6 + - - -
84A ALA* 3.5 5.2 - - - -
85A ALA* 2.9 42.5 + - - -
87A THR* 4.6 1.2 + - - -
218A PHE* 3.5 24.1 - - - -
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Residues in contact with ARG 58 (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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56A ILE* 4.0 12.1 - - + +
57A SER* 1.3 77.1 - - - +
59A TYR* 1.3 63.4 + - - +
60A ASN 4.1 0.6 + - - -
66A ILE* 3.3 7.7 - - - +
67A ARG* 2.9 44.7 + - + +
69A HIS* 5.5 7.4 + - + -
80A SER* 2.6 32.5 + - - -
81A LEU* 3.9 12.3 - - - +
82A TYR 3.6 21.2 + - - -
83A GLY 5.1 3.1 - - - -
84A ALA* 3.7 23.7 - - + +
218A PHE* 4.3 2.5 - - - -
289A ASP* 4.2 15.2 + - - -
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Residues in contact with TYR 59 (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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58A ARG* 1.3 77.3 - - - +
60A ASN* 1.3 58.0 + - - +
61A PRO* 3.3 32.8 - - + +
64A LYS* 3.3 36.0 + - - +
65A ARG 3.8 18.4 - - - -
66A ILE* 3.6 23.1 - - + -
83A GLY 5.3 2.2 + - - -
218A PHE* 3.8 21.5 - - + -
222A LEU* 5.0 1.3 - - + +
223A MET* 3.5 52.3 - - + +
226A ALA* 3.6 25.1 - - + +
227A GLU* 4.2 9.6 + - + +
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Residues in contact with ASN 60 (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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58A ARG* 4.1 1.4 + - - +
59A TYR* 1.3 72.4 - - - +
61A PRO* 1.3 68.5 - - - +
62A ILE* 3.6 16.6 - - - +
63A THR* 2.5 35.7 + - - +
64A LYS* 2.9 26.0 + - - -
65A ARG 3.3 15.0 + - - +
67A ARG* 6.2 2.6 - - + +
290A ARG* 3.4 43.8 + - - +
292A GLU* 5.1 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