Contacts of the strand formed by residues 132 - 141 (chain L) in PDB entry 5G04
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 132 (chain L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1455A GLU* 5.7 4.0 - - - +
73L THR* 3.5 1.0 - - - -
74L VAL* 3.0 39.7 + - - +
98L VAL* 4.5 16.3 - - + +
108L ILE* 4.9 3.9 - - + +
124L LEU* 3.5 27.1 + - - +
125L THR 3.9 5.5 + - - +
126L ASP* 3.4 36.3 - - + +
131L PRO* 1.3 70.4 - - - +
133L ARG* 1.3 62.0 + - - +
134L THR* 4.6 6.9 - - - +
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Residues in contact with ARG 133 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1397A ASP* 5.5 7.2 - - - -
1452A LEU* 6.3 0.4 - - - +
1453A ASN* 3.2 43.6 + - - +
1455A GLU* 3.5 16.1 + - - +
71L LYS* 3.4 48.4 + - + +
72L THR 4.0 2.5 - - - -
73L THR* 2.8 38.8 + - - +
130L LYS* 6.0 0.8 - - - +
131L PRO* 3.6 17.3 + - - +
132L THR* 1.3 71.6 - - - +
134L THR* 1.3 61.8 + - - +
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Residues in contact with THR 134 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68L PHE* 4.0 6.1 - - - -
71L LYS* 3.9 11.7 + - - +
72L THR 3.3 24.3 + - - +
74L VAL* 4.1 9.9 - - + -
98L VAL* 3.6 31.1 - - + +
99L GLY* 3.3 29.3 + - - -
100L ASN* 5.2 0.5 + - - -
132L THR* 4.6 4.5 - - - -
133L ARG* 1.3 76.6 - - - +
135L PHE* 1.3 64.1 + - - +
136L MET 3.6 1.8 + - - +
137L ILE* 3.9 24.9 - - + -
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Residues in contact with PHE 135 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1361A ASP* 5.5 2.9 - - - +
1396A LEU 4.9 0.4 - - - -
1397A ASP 3.3 20.6 - - - -
1398A PHE 3.7 8.7 - - - -
1399A VAL 3.2 23.8 - - - -
1400A LYS* 3.4 29.2 - - + +
1401A PRO* 3.4 22.0 - - + -
1456A THR* 5.9 0.9 - - + -
67L GLN* 3.5 4.4 - - + +
68L PHE* 2.8 48.3 + - - +
69L ARG 4.8 1.3 - - - -
70L ARG 4.7 0.7 - - - -
71L LYS* 3.6 41.9 - - + +
99L GLY 3.7 10.0 + - - +
100L ASN* 3.8 21.5 + - + +
134L THR* 1.3 75.6 + - - +
136L MET* 1.3 58.6 + - + +
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Residues in contact with MET 136 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1400A LYS* 5.4 0.2 - - - +
65L ASN* 3.7 19.3 - - + +
66L ILE 3.2 8.3 - - - +
67L GLN* 4.2 12.3 - - + +
98L VAL* 3.3 8.8 - - - +
99L GLY 3.2 32.5 + - - +
100L ASN 3.7 20.2 - - - +
102L PHE* 3.6 53.2 - - + -
105L LEU* 3.5 37.5 - - + -
134L THR* 3.5 2.0 + - - -
135L PHE* 1.3 80.3 - - - +
137L ILE* 1.3 69.2 + - - +
138L GLN* 3.7 0.4 - - - +
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Residues in contact with ILE 137 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64L VAL 3.6 0.5 - - - +
65L ASN* 3.5 2.8 - - - -
66L ILE* 2.7 48.0 + - + +
68L PHE* 3.5 30.3 - - + -
74L VAL* 3.7 32.1 - - + -
77L LEU* 5.3 1.3 - - + -
96L VAL* 4.7 10.5 - - + -
97L ARG 3.5 4.7 - - - +
98L VAL* 3.8 17.3 - - + -
124L LEU* 4.7 5.2 - - + -
134L THR* 3.9 6.5 - - + -
136L MET* 1.3 80.2 - - - +
138L GLN* 1.3 69.8 + - - +
139L ILE* 4.0 20.0 - - + -
158L ILE* 4.0 16.8 - - + -
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Residues in contact with GLN 138 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63L LEU* 3.1 41.3 - - + +
64L VAL 3.8 3.8 - - - +
65L ASN* 3.0 34.8 + - - +
95L SER 3.7 0.9 - - - +
96L VAL* 3.4 7.6 - - - +
97L ARG* 2.7 58.1 + - + +
102L PHE* 4.6 4.7 - - - +
105L LEU* 3.0 32.3 - - + +
136L MET* 3.7 1.1 - - + +
137L ILE* 1.3 75.5 - - - +
139L ILE* 1.3 67.5 + - - +
140L ALA* 3.8 0.6 - - - +
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Residues in contact with ILE 139 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62L HIS 3.5 1.7 - - - +
63L LEU* 3.2 6.9 - - - -
64L VAL* 2.9 47.5 + - + +
66L ILE* 3.8 28.7 - - + -
77L LEU* 3.9 32.3 - - + -
79L ILE* 3.8 26.7 - - + -
94L ILE* 4.6 14.6 - - + -
95L SER 3.6 4.9 - - - +
96L VAL* 5.1 2.2 - - + -
137L ILE* 4.0 10.3 - - + -
138L GLN* 1.3 80.3 - - - +
140L ALA* 1.3 59.1 + - - +
141L VAL* 4.7 0.2 - - - +
153L MET* 4.0 10.8 - - + -
156L ILE* 4.7 4.7 - - + -
158L ILE* 5.6 0.4 - - + -
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Residues in contact with ALA 140 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61L PRO* 4.7 0.4 - - + -
62L HIS 3.5 4.5 - - - -
63L LEU* 3.6 20.0 - - + -
94L ILE* 3.5 4.6 - - - +
95L SER* 2.8 45.2 + - - +
97L ARG* 3.8 32.1 - - - +
138L GLN* 3.8 0.8 - - - +
139L ILE* 1.3 73.6 - - - +
141L VAL* 1.3 61.2 + - - +
142L LEU* 3.5 10.0 + - + -
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Residues in contact with VAL 141 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54L TRP* 5.3 2.0 - - + -
60L GLN* 3.6 7.3 - - - +
61L PRO* 3.5 17.6 - - - +
62L HIS* 2.9 28.0 + - + +
91L PRO* 3.8 13.5 - - + -
92L SER 4.8 0.2 - - - +
93L LYS 4.6 1.1 - - - -
94L ILE* 4.5 7.0 - - + -
139L ILE* 4.7 2.9 - - + +
140L ALA* 1.3 72.0 - - - +
142L LEU* 1.3 64.5 + - - +
143L ALA 3.4 9.3 + - - +
144L ASN* 3.6 9.0 - - - +
151L THR* 3.6 39.0 - - + +
153L MET* 3.6 28.3 - - + -
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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