Contacts of the strand formed by residues 68 - 75 (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 GLU 68 (chain Q).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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9L ASN* 5.6 1.4 + - - +
64L ARG* 3.2 38.6 + - - +
79L PHE* 3.6 7.8 - - - +
80L ASP* 5.2 1.6 - - + -
81L GLY* 3.0 39.4 + - - +
101L GLY* 5.5 0.4 - - - -
102L PRO* 3.9 15.2 - - + +
64Q ILE* 4.1 3.3 - - - +
65Q SER 2.9 36.3 + - - +
66Q ASN 3.0 5.1 + - - +
67Q GLY* 1.3 80.3 - - - +
69Q GLY* 1.3 76.6 + - - +
70Q VAL* 3.5 4.7 + - - +
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Residues in contact with GLY 69 (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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79L PHE* 3.4 7.6 - - - -
80L ASP* 3.2 47.9 + - - +
62Q ARG* 4.6 2.5 - - - -
63Q LYS 3.7 5.8 - - - -
64Q ILE* 3.8 14.0 - - - +
67Q GLY 4.2 1.0 + - - -
68Q GLU* 1.3 78.1 - - - +
70Q VAL* 1.3 64.1 + - - +
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Residues in contact with VAL 70 (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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77L ILE* 4.6 3.4 - - + -
78L ARG 3.7 2.2 - - - -
79L PHE* 3.7 27.6 - - + -
102L PRO* 3.9 18.6 - - + -
123L LEU* 4.2 9.0 - - + -
43Q PHE* 3.6 29.4 - - + -
61Q VAL 3.9 0.3 - - - +
62Q ARG* 3.3 4.0 - - - +
63Q LYS* 2.9 47.0 + - + +
65Q SER* 4.5 8.1 - - - +
68Q GLU* 3.8 9.9 - - - +
69Q GLY* 1.3 79.7 - - - +
71Q GLU* 1.3 68.5 + - - +
72Q ARG 4.0 0.3 + - - -
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Residues in contact with GLU 71 (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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76L VAL 3.9 0.4 - - - +
77L ILE* 3.6 4.5 - - - +
78L ARG* 3.0 75.4 + - + +
80L ASP* 4.5 5.7 - - - +
48Q ILE* 4.2 7.5 - - + +
60Q THR* 4.3 9.0 - - + +
61Q VAL 3.3 7.6 - - - +
62Q ARG* 3.7 26.2 + - + +
69Q GLY 4.2 0.2 - - - -
70Q VAL* 1.3 75.0 - - - +
72Q ARG* 1.3 61.9 + - - +
73Q VAL* 4.2 1.3 - - + +
101Q ARG* 2.7 48.4 + - - +
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Residues in contact with ARG 72 (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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71L ARG* 4.1 29.1 - - - +
75L SER* 4.6 8.7 + - - -
76L VAL 3.3 13.9 - - - +
77L ILE* 3.6 30.3 - - + +
123L LEU* 4.0 15.9 + - - +
30Q VAL* 4.4 22.4 - - - +
32Q VAL* 5.4 2.6 - - - +
41Q GLN* 4.5 12.1 - - - +
43Q PHE* 3.7 33.1 - - + +
59Q PHE 3.9 0.2 - - - +
60Q THR* 4.6 0.7 - - - -
61Q VAL* 2.9 32.6 + - - +
70Q VAL* 4.0 1.5 + - + -
71Q GLU* 1.3 75.6 - - - +
73Q VAL* 1.3 64.7 + - - +
74Q PHE* 3.2 43.6 + - + -
80Q VAL* 5.3 4.6 - - - +
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Residues in contact with VAL 73 (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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2684A U 4.2 25.4 - - - +
2685A G 3.9 8.7 - - - +
74L GLY 5.7 1.1 - - - +
75L SER* 3.4 10.2 + - - -
76L VAL* 2.8 46.6 + - + +
78L ARG* 3.8 24.0 - - + +
58Q ALA* 4.7 3.6 - - + -
59Q PHE 3.6 10.8 - - - +
60Q THR* 3.4 22.4 - - + +
71Q GLU* 5.7 1.3 - - + -
72Q ARG* 1.3 76.3 - - - +
74Q PHE* 1.3 70.8 + - - +
75Q GLN* 5.5 2.0 - - - +
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Residues in contact with PHE 74 (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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75L SER* 4.0 7.4 - - - -
28Q VAL* 4.2 14.8 - - + -
30Q VAL* 4.1 11.9 - - + -
43Q PHE* 3.6 36.3 - + + -
58Q ALA* 3.4 5.5 - - - +
59Q PHE* 2.9 69.2 + + + -
61Q VAL* 4.2 4.5 - - + -
72Q ARG* 3.2 58.8 - - - -
73Q VAL* 1.3 79.5 - - - +
75Q GLN* 1.3 64.8 + - - +
76Q THR 3.7 0.3 + - - -
80Q VAL* 6.2 0.9 - - + -
81Q VAL* 4.0 19.7 - - + -
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Residues in contact with GLN 75 (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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2683A C 3.0 31.6 + - - -
2684A U 4.0 2.3 + - - -
13D ARG* 3.1 30.8 + - - +
15D PHE* 4.6 6.3 - - + -
73L ASP* 3.5 25.3 + - - +
74L GLY* 3.7 13.3 - - - +
75L SER* 4.0 5.2 + - - +
56Q HIS 4.3 0.8 + - - -
57Q SER 4.1 3.8 + - - +
58Q ALA* 3.5 23.2 - - - +
73Q VAL* 5.5 1.9 - - + +
74Q PHE* 1.3 73.2 + - - +
76Q THR* 1.3 68.1 + - - +
77Q HIS 3.5 0.9 - - - -
78Q SER* 3.2 29.3 - - - +
81Q VAL* 3.9 12.1 - - - +
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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