Contacts of the strand formed by residues 58 - 65 (chain Q) 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 ALA 58 (chain Q).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2684A U 3.6 16.6 - - - +
50Q ILE* 3.9 2.3 - - - +
51Q ARG* 2.9 41.3 + - + +
56Q HIS 3.4 4.2 + - - +
57Q SER* 1.3 76.1 - - - +
59Q PHE* 1.3 66.6 + - - +
73Q VAL* 4.7 5.6 - - + -
74Q PHE 3.4 8.5 - - - +
75Q GLN* 3.5 22.4 - - - +
76Q THR* 3.9 3.8 + - - -
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Residues in contact with PHE 59 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20Q PHE* 4.2 22.2 - + + -
26Q VAL* 5.0 2.5 - - + -
28Q VAL* 3.8 18.8 - - + -
47Q VAL* 4.1 11.9 - - + -
49Q ALA* 3.2 17.9 - - - +
50Q ILE* 4.3 5.2 - - + -
58Q ALA* 1.3 76.4 - - - +
60Q THR* 1.3 60.3 + - - +
61Q VAL* 3.3 36.1 - - + -
72Q ARG 3.9 0.9 - - - +
73Q VAL* 4.4 2.5 - - - -
74Q PHE* 2.9 62.0 + + + +
76Q THR* 3.6 24.9 - - - +
81Q VAL* 5.4 1.8 - - + -
84Q ILE* 3.7 30.1 - - + -
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Residues in contact with THR 60 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2685A G 4.2 7.4 + - - -
78L ARG* 4.4 3.3 + - - +
47Q VAL* 3.6 2.8 - - - -
48Q ILE* 2.9 48.9 + - + -
49Q ALA* 3.0 28.6 + - - +
59Q PHE* 1.3 71.2 - - - +
61Q VAL* 1.3 69.0 + - - +
71Q GLU* 4.3 19.3 - - + +
72Q ARG 3.8 6.3 - - - +
73Q VAL* 3.4 24.1 - - + +
98Q TYR* 5.9 0.7 - - + -
101Q ARG* 5.4 0.9 - - - +
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Residues in contact with VAL 61 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26Q VAL* 4.6 4.5 - - + +
28Q VAL* 4.9 4.0 - - + -
43Q PHE* 4.3 13.3 - - + +
45Q GLY* 3.4 38.6 - - - +
46Q VAL 3.6 4.7 - - - +
47Q VAL* 3.7 11.9 - - + +
59Q PHE* 3.3 37.7 - - + -
60Q THR* 1.3 75.6 - - - +
62Q ARG* 1.3 65.9 + - - +
70Q VAL 3.9 0.2 - - - +
71Q GLU* 3.3 4.3 - - - +
72Q ARG 2.9 35.3 + - - +
74Q PHE* 4.2 13.2 - - + -
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Residues in contact with ARG 62 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80L ASP* 3.0 40.0 + - - -
43Q PHE* 5.3 0.2 - - - -
45Q GLY* 3.4 1.2 - - - -
46Q VAL* 2.9 40.2 + - + +
48Q ILE* 4.2 27.6 - - + -
61Q VAL* 1.3 77.7 - - - +
63Q LYS* 1.3 67.7 + - - +
64Q ILE* 4.3 21.6 - - + +
69Q GLY* 4.6 3.2 - - - -
70Q VAL 3.3 8.7 - - - +
71Q GLU* 3.7 25.6 + - + +
100Q LEU* 3.3 35.8 + - - +
101Q ARG* 3.7 14.4 + - - +
103Q ARG 5.0 1.8 + - - -
104Q THR* 6.2 1.0 - - - +
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Residues in contact with LYS 63 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121L GLU* 3.5 16.4 + - - -
42Q ALA 4.5 4.0 + - - -
43Q PHE* 3.3 56.8 - - + +
44Q GLU 3.1 28.5 - - - +
45Q GLY* 3.9 2.7 - - - -
62Q ARG* 1.3 77.2 - - - +
64Q ILE* 1.3 70.4 + - - +
65Q SER* 3.1 24.5 - - - +
69Q GLY* 3.7 0.2 - - - -
70Q VAL* 2.9 37.8 + - + +
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Residues in contact with ILE 64 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62Q ARG* 4.3 19.7 - - + +
63Q LYS* 1.3 81.3 - - - +
65Q SER* 1.3 63.9 + - - +
66Q ASN 4.2 1.0 + - - -
67Q GLY* 4.0 30.7 - - - +
68Q GLU 3.7 1.1 - - - -
69Q GLY* 3.8 17.5 - - - +
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Residues in contact with SER 65 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102L PRO* 3.6 17.2 - - - +
121L GLU* 3.1 24.3 + - - -
63Q LYS* 3.1 32.5 + - - +
64Q ILE* 1.3 74.8 + - - +
66Q ASN* 1.3 75.9 + - - +
67Q GLY 3.3 0.4 - - - -
68Q GLU 2.9 23.2 + - - +
70Q VAL* 4.5 4.3 - - - -
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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