Contacts of the strand formed by residues 101 - 106 (chain N) in PDB entry 5GAG
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 VAL 101 (chain N).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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23N GLY 3.4 10.0 + - - +
24N THR 3.4 35.2 - - - +
25N ASP 3.9 9.6 - - - +
26N VAL* 5.2 1.1 - - + -
32N GLY* 4.7 4.7 - - - -
33N LEU 3.8 10.3 - - - +
34N LYS* 3.8 14.6 - - + -
66N ARG* 3.1 28.5 + - - +
100N LYS* 1.3 82.8 - - - +
102N LEU* 1.3 58.8 + - - +
103N TYR 4.0 18.4 - - - +
104N GLU* 4.0 22.2 - - + +
131N VAL* 5.0 5.2 - - + -
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Residues in contact with LEU 102 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33N LEU* 3.2 20.0 + - + +
35N ALA* 3.7 31.0 - - + -
41N LEU* 4.3 10.8 - - + -
65N ILE* 3.4 7.3 - - - +
66N ARG* 2.7 28.3 + - - +
67N VAL* 3.8 28.5 - - + -
96N ILE* 3.9 18.6 - - + -
100N LYS* 4.2 6.7 - - + +
101N VAL* 1.3 75.3 - - - +
103N TYR* 1.3 71.8 + - + +
124N LEU* 3.7 29.8 - - + -
126N ILE* 4.5 1.8 - - + -
128N THR* 4.5 6.1 - - + -
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Residues in contact with TYR 103 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32N GLY* 3.2 5.4 - - - -
33N LEU* 2.9 49.1 + - + -
41N LEU* 6.4 0.9 - - + -
46N ILE* 2.9 42.3 + - + +
49N ALA* 3.6 14.1 - - + +
50N ARG* 3.6 7.2 + - + -
53N MET* 3.5 33.0 - - + -
63N ILE* 4.9 0.7 - - + -
64N TRP 3.5 11.0 - - - -
65N ILE* 3.5 31.9 - - + -
67N VAL* 6.0 0.7 - - + -
101N VAL* 4.0 1.6 - - - +
102N LEU* 1.3 90.9 - - + +
104N GLU* 1.3 65.2 + - - +
117N PHE* 3.8 19.6 - - + -
124N LEU* 4.4 12.8 - - + -
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Residues in contact with GLU 104 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25N ASP 3.6 0.3 - - - +
26N VAL* 3.3 11.6 - - + +
27N SER 2.9 11.9 + - - -
28N PHE* 2.8 17.1 + - - +
29N GLY 2.7 31.2 + - - -
31N PHE 3.3 7.9 - - - +
32N GLY* 5.0 0.2 - - - -
63N ILE* 3.4 4.5 - - - +
64N TRP* 2.9 46.6 + - + +
66N ARG* 2.3 44.2 + - + +
101N VAL* 4.0 13.0 - - + +
103N TYR* 1.3 80.0 - - - +
105N MET* 1.3 64.9 + - - +
117N PHE* 4.2 2.7 - - - -
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Residues in contact with MET 105 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29N GLY* 4.0 3.1 - - - -
30N SER 3.1 2.4 + - - -
31N PHE* 3.0 39.7 + - + -
53N MET* 4.2 8.5 - - + -
57N VAL* 4.2 17.3 - - + -
62N LYS 3.2 11.9 - - - +
63N ILE* 3.7 25.4 - - + -
64N TRP* 3.9 2.0 - - - -
104N GLU* 1.3 79.2 - - - +
106N ASP* 1.3 63.0 + - - +
108N VAL* 4.0 17.3 - - + -
113N ALA* 3.7 28.3 - - - +
116N ALA* 4.6 2.2 - - + -
117N PHE* 3.5 33.8 - - + -
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Residues in contact with ASP 106 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28N PHE 5.3 1.0 - - - +
29N GLY* 3.8 3.1 - - - -
30N SER* 3.4 28.9 + - - +
31N PHE* 4.9 2.5 - - - -
61N GLY* 3.3 3.1 - - - -
62N LYS* 2.9 38.4 + - - +
64N TRP* 3.2 25.1 - - - -
105N MET* 1.3 79.5 - - - +
107N GLY* 1.3 67.1 + - - +
108N VAL* 3.3 9.5 + - - +
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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