Contacts of the strand formed by residues 50 - 56 (chain t) 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 t).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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45t LYS 3.9 0.2 - - - -
46t LEU* 2.9 44.3 + - + -
47t THR* 3.1 24.3 + - - +
48t ASP 3.7 0.8 - - - -
49t LYS* 1.3 81.8 + - - +
51t VAL* 1.3 68.3 + - - +
83t MET 5.1 0.3 + - - -
84t THR 4.8 0.3 - - - -
85t THR* 2.7 33.0 + - + +
88t ILE* 4.2 11.3 - - + +
110t ILE* 3.8 27.6 - - + -
111t GLY 3.7 3.1 - - - +
203t ILE* 4.8 0.2 - - - +
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Residues in contact with VAL 51 (chain t).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23t VAL* 4.1 18.0 - - + +
43t CYS* 4.5 1.6 - - + -
44t TYR 3.4 19.7 - - - +
45t LYS* 4.7 2.5 - - + +
50t THR* 1.3 82.6 - - - +
52t ILE* 1.3 70.8 + - - +
109t ILE 4.0 0.3 - - - +
110t ILE* 3.6 3.1 - - - +
111t GLY 2.8 36.2 + - - +
196t CYS* 4.2 22.7 - - + -
198t VAL* 3.6 24.5 - - + -
203t ILE* 3.8 24.7 - - + -
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Residues in contact with ILE 52 (chain t).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23t VAL* 4.6 0.4 - - - -
42t LYS 3.6 0.9 - - - +
43t CYS* 3.5 2.3 - - - -
44t TYR* 2.8 61.1 + - + +
46t LEU* 3.8 26.9 - - + +
51t VAL* 1.3 77.9 - - - +
53t GLY* 1.3 69.7 + - - +
54t CYS* 3.8 7.0 - - - -
65t THR* 5.3 2.0 - - - +
68t ILE* 3.8 25.1 - - + -
88t ILE* 6.0 0.4 - - + -
92t LEU* 4.3 3.4 - - + -
108t ASN* 3.4 27.6 - - + +
109t ILE 3.6 3.8 - - - +
110t ILE* 3.9 20.9 - - + +
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Residues in contact with GLY 53 (chain t).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12t ILE* 3.4 24.5 - - - +
23t VAL* 4.2 10.7 - - - +
42t LYS 3.2 10.5 - - - -
43t CYS* 4.5 0.9 - - - -
52t ILE* 1.3 72.3 - - - +
54t CYS* 1.3 60.3 + - - +
107t TYR 3.7 0.7 - - - +
108t ASN* 3.2 5.7 - - - +
109t ILE 2.9 38.3 + - - -
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Residues in contact with CYS 54 (chain t).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12t ILE* 3.3 2.2 - - - +
42t LYS* 3.0 31.2 + - - +
44t TYR* 4.2 14.9 + - + -
52t ILE* 3.8 15.9 - - - -
53t GLY* 1.3 75.3 - - - -
55t SER* 1.3 60.9 + - - +
61t CYS* 3.7 27.1 - - + +
64t LEU* 5.2 4.3 - - - -
65t THR* 4.1 19.7 - - - -
68t ILE* 5.7 0.7 - - - -
106t VAL* 4.1 4.7 - - + -
107t TYR 3.5 3.6 - - - -
108t ASN* 3.0 24.7 - - - +
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Residues in contact with SER 55 (chain t).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7t PHE* 5.4 0.7 - - - -
9t GLY 3.4 11.0 + - - -
10t GLY* 3.0 27.2 + - - -
12t ILE* 3.6 19.2 - - - +
42t LYS* 5.2 3.4 - - - -
54t CYS* 1.3 75.6 - - - +
56t GLY* 1.3 61.8 + - - +
61t CYS* 4.0 5.6 - - - -
106t VAL* 3.6 4.7 - - - +
107t TYR* 2.9 39.1 + - - +
138t GLY 5.2 0.4 - - - -
139t GLY* 3.9 15.9 - - - -
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Residues in contact with GLY 56 (chain t).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7t PHE* 4.3 20.2 - - - -
8t ASN* 3.2 34.2 + - - +
9t GLY 4.0 4.9 + - - +
55t SER* 1.3 82.8 + - - +
57t PHE* 1.3 63.2 + - - -
58t HIS 3.5 0.3 + - - -
61t CYS* 4.3 1.4 - - - -
105t TYR* 3.7 7.2 - - - -
107t TYR* 5.0 6.7 - - - -
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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