Contacts of the strand formed by residues 50 - 56 (chain f) in PDB entry 5GJQ
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 50 (chain f).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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46f LEU* 2.9 31.4 + - + +
47f THR* 3.1 23.6 + - - +
48f ASP 3.7 1.8 - - - -
49f LYS* 1.3 80.9 - - - +
51f VAL* 1.3 70.0 + - - +
83f MET 4.9 0.2 + - - -
84f THR 4.6 1.0 - - - -
85f THR* 2.8 32.4 + - + -
88f ILE* 4.1 21.3 - - + +
110f ILE* 3.7 28.5 - - + -
111f GLY 3.6 2.9 - - - +
203f ILE* 4.9 0.4 - - - +
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Residues in contact with VAL 51 (chain f).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23f VAL* 4.2 18.6 - - + +
43f CYS* 4.1 13.7 - - + -
44f TYR 3.3 26.5 - - - +
45f LYS* 4.5 2.7 - - - -
46f LEU* 5.1 0.2 - - - -
50f THR* 1.3 79.0 - - - +
52f ILE* 1.3 67.0 + - - +
109f ILE 4.0 0.5 - - - +
110f ILE* 3.5 3.5 - - - +
111f GLY 2.9 35.3 + - - +
196f CYS* 4.7 8.1 - - + -
198f VAL* 3.8 23.6 - - + -
203f ILE* 3.9 24.2 - - + -
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Residues in contact with ILE 52 (chain f).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23f VAL* 5.1 0.7 - - - -
43f CYS* 3.5 1.6 - - - -
44f TYR* 2.9 46.6 + - + +
46f LEU* 3.7 36.8 - - + +
51f VAL* 1.3 78.3 - - - +
53f GLY* 1.3 66.6 + - - +
54f CYS* 3.8 11.2 - - - -
65f THR* 5.1 3.1 - - - +
68f ILE* 3.8 26.2 - - + -
88f ILE* 6.1 0.2 - - + -
92f LEU* 4.0 12.3 - - + -
108f ASN* 3.4 22.9 - - + +
109f ILE 3.6 5.2 - - - +
110f ILE* 3.9 15.3 - - + -
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Residues in contact with GLY 53 (chain f).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12f ILE* 3.5 20.7 - - - +
23f VAL* 4.8 6.4 - - - +
42f LYS 3.3 9.4 - - - -
43f CYS* 4.5 2.5 - - - -
52f ILE* 1.3 74.2 - - - +
54f CYS* 1.3 62.5 + - - -
107f TYR 3.6 0.9 - - - +
108f ASN* 3.3 7.6 - - - +
109f ILE 2.8 36.9 + - - -
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Residues in contact with CYS 54 (chain f).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12f ILE* 3.3 4.4 - - - +
42f LYS* 3.0 31.1 + - - +
44f TYR* 4.4 14.3 + - + -
52f ILE* 3.8 15.9 - - - -
53f GLY* 1.3 75.0 - - - -
55f SER* 1.3 59.5 + - - +
58f HIS* 5.8 0.5 + - - -
61f CYS* 3.8 30.5 - - + +
64f LEU* 4.8 6.3 - - - -
65f THR* 4.2 17.7 - - - -
68f ILE* 5.9 0.2 - - - -
106f VAL* 4.1 4.7 - - + -
107f TYR 3.7 3.6 - - - -
108f ASN* 3.1 22.2 - - - +
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Residues in contact with SER 55 (chain f).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7f PHE* 5.9 0.9 - - - -
9f GLY 3.4 8.5 + - - -
10f GLY* 3.0 27.9 + - - -
12f ILE* 3.6 18.6 - - - +
42f LYS* 5.5 2.0 - - - -
54f CYS* 1.3 76.5 - - - +
56f GLY* 1.3 61.2 + - - +
61f CYS* 4.1 4.3 - - - -
106f VAL* 3.4 4.9 - - - +
107f TYR* 2.9 42.0 + - - +
138f GLY 4.9 0.7 - - - -
139f GLY* 3.8 17.5 - - - -
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Residues in contact with GLY 56 (chain f).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6f VAL 4.9 0.2 - - - -
7f PHE* 4.9 13.9 - - - -
8f ASN* 3.1 34.5 + - - +
9f GLY 3.9 5.9 + - - +
55f SER* 1.3 81.5 + - - +
57f PHE* 1.3 63.5 + - - -
58f HIS* 3.4 1.0 + - - -
61f CYS* 4.2 2.5 - - - -
105f TYR* 3.6 10.3 - - - -
107f TYR* 5.1 6.1 - - - -
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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