Contacts of the strand formed by residues 70 - 78 (chain T) in PDB entry 5GAH
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 LYS 70 (chain T).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26T GLY* 4.2 13.7 - - - +
27T LYS 3.4 9.4 - - - +
28T LYS* 4.0 20.3 - - + +
29T VAL* 4.3 1.8 - - - -
68T ASP 4.1 10.3 + - - +
69T LEU* 1.3 77.7 - - - +
71T VAL* 1.3 66.2 + - - +
72T THR* 3.5 5.8 + - + -
107T VAL* 3.3 9.0 - - - +
108T SER 3.1 31.5 + - - +
109T ASP 4.5 3.4 + - - -
110T ARG 4.0 19.0 + - - +
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Residues in contact with VAL 71 (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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24T ILE* 4.1 29.6 - - + +
25T ARG* 4.2 1.4 - - - +
26T GLY* 3.1 22.7 + - - -
27T LYS 3.0 15.9 + - - +
29T VAL* 4.1 16.2 - - + -
32T ALA* 4.7 7.2 - - + -
51T LEU* 4.2 13.9 - - + -
70T LYS* 1.3 74.8 - - - +
72T THR* 1.3 63.2 + - - +
73T LYS 4.6 0.4 - - - +
74T ILE* 3.6 33.0 - - + -
105T VAL* 4.4 11.7 - - + -
106T VAL 4.1 8.3 - - - +
107T VAL* 4.6 1.3 - - + -
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Residues in contact with THR 72 (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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520A G 5.9 1.9 - - - +
2T GLU* 4.7 7.5 + - - -
25T ARG* 4.8 9.2 + - - +
70T LYS* 4.1 9.4 - - + +
71T VAL* 1.3 75.9 - - - +
73T LYS* 1.3 78.9 + - - +
74T ILE* 4.3 0.8 + - - -
106T VAL* 3.0 23.6 + - - +
108T SER* 3.0 41.5 - - - +
110T ARG* 4.5 5.2 - - - +
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Residues in contact with LYS 73 (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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519A U 4.1 18.2 - - - +
520A G 5.4 13.9 - - - -
2T GLU* 3.8 21.8 + - - +
25T ARG* 5.5 1.1 - - - +
71T VAL* 4.7 0.4 - - - -
72T THR* 1.3 96.3 + - - +
74T ILE* 1.3 61.2 + - - +
75T PHE* 4.1 19.8 - - + -
104T THR 3.8 1.7 - - - +
105T VAL 3.7 0.9 - - - -
106T VAL* 2.9 40.9 + - + +
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Residues in contact with ILE 74 (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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519A U 4.7 1.1 + - - +
21T ALA* 3.4 46.9 - - + +
24T ILE* 3.5 23.1 - - + -
25T ARG* 2.5 59.6 + - + +
47T VAL* 4.3 7.2 - - + -
71T VAL* 3.6 24.5 - - + -
73T LYS* 1.3 75.0 - - - +
75T PHE* 1.3 61.3 + - - +
76T VAL* 5.3 0.9 - - + -
103T ILE* 5.4 2.9 - - + -
104T THR 3.3 5.6 - - - +
105T VAL* 4.1 18.2 - - + -
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Residues in contact with PHE 75 (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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23A G 4.7 10.5 - - - -
518A G 4.4 11.9 - - - +
519A U 3.9 32.1 - - - +
21T ALA* 5.5 0.2 - - - -
25T ARG* 4.6 1.6 - - - +
73T LYS* 4.1 25.8 - - + -
74T ILE* 1.3 83.9 - - - +
76T VAL* 1.3 66.2 + - - +
77T ASP* 3.4 29.2 - - - +
102T HIS 3.4 1.9 - - - +
104T THR* 2.9 59.8 + - + -
106T VAL* 5.2 4.9 - - + -
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Residues in contact with VAL 76 (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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518A G 3.6 7.5 + - - -
14T ALA* 4.0 6.5 - - - +
17T VAL* 3.8 34.3 - - + -
18T ARG* 3.3 40.7 + - + +
21T ALA* 3.7 27.8 - - + -
75T PHE* 1.3 79.4 - - - +
77T ASP* 1.3 63.1 + - - +
101T SER* 3.8 21.5 - - - +
102T HIS 3.3 11.0 - - - +
103T ILE* 4.3 10.3 - - + -
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Residues in contact with ASP 77 (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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23A G 4.0 21.1 + - - +
24A G 3.6 36.2 - - - +
517A C 5.7 0.7 - - - -
518A G 4.1 9.2 + - - +
14T ALA* 3.8 5.1 - - - +
18T ARG* 4.9 2.0 - - - +
75T PHE* 3.4 33.3 - - - -
76T VAL* 1.3 77.8 - - - +
78T GLU* 1.3 63.5 + - - +
101T SER* 3.2 11.3 - - - -
102T HIS* 3.0 42.3 + - + +
104T THR* 4.1 3.3 + - - -
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Residues in contact with GLU 78 (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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24A G 2.6 45.0 + - - +
25A U 3.7 19.4 + - - +
516A C 4.3 2.8 + - - +
517A C 3.4 46.5 + - - +
1261A C 4.3 4.0 - - - +
1262A A 3.1 27.6 + - - +
14T ALA* 4.3 12.5 - - + +
77T ASP* 1.3 77.2 - - - +
79T GLY* 1.3 64.7 + - - +
99T ARG* 4.7 4.2 + - - -
100T THR 4.3 3.1 - - - +
101T SER* 4.2 0.4 - - - -
102T HIS* 3.7 4.4 - - - -
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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