Contacts of the strand formed by residues 68 - 78 (chain B) in PDB entry 5F0L
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 ILE 68 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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52B VAL* 5.6 1.1 - - + -
54B LEU* 3.9 22.7 - - + -
65B HIS* 3.6 24.0 - - + +
67B GLY* 1.3 77.7 - - - +
69B ARG* 1.3 70.5 - - - +
94B GLU* 3.8 4.3 - - - +
95B LEU* 2.9 35.4 + - + -
96B ALA* 3.0 20.9 + - + +
101B LEU* 4.0 9.4 - - + -
107B TYR* 3.8 26.9 - - + +
134B VAL* 4.5 6.3 - - + -
135B THR 3.4 5.2 - - - +
136B ILE* 3.9 27.6 - - + -
409B EDO 4.5 0.4 - - - -
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Residues in contact with ARG 69 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68B ILE* 1.3 73.4 - - - +
70B ILE* 1.3 61.1 + - - +
71B GLU* 3.0 35.0 + - + -
92B VAL* 3.6 24.0 - - + -
93B LYS 3.6 10.8 - - - +
94B GLU* 3.5 19.0 + - - +
95B LEU* 3.8 6.7 - - - +
133B LYS* 5.5 0.4 - - - +
134B VAL* 3.5 9.7 - - - +
135B THR* 3.0 53.6 + - - +
137B VAL* 3.7 24.4 - - - +
142B ASP* 5.0 2.4 + - - -
409B EDO 3.2 20.7 + - - +
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Residues in contact with ILE 70 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16B ILE* 4.5 2.2 - - + -
52B VAL* 3.7 10.1 - - + -
69B ARG* 1.3 75.6 - - - +
71B GLU* 1.3 74.4 + - - +
92B VAL* 3.6 1.9 - - - +
93B LYS* 2.9 55.3 + - + +
95B LEU* 3.7 17.3 - - + -
109B PHE* 3.6 52.9 - - + -
111B PHE* 3.6 6.5 - - + -
132B LEU* 4.3 12.6 - - + -
133B LYS 3.5 5.8 - - - +
134B VAL* 3.7 16.2 - - + -
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Residues in contact with GLU 71 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69B ARG* 3.0 41.3 + - - -
70B ILE* 1.3 78.1 - - - +
72B PHE* 1.3 58.7 + - - +
73B VAL* 3.9 12.7 + - + -
90B ASN* 3.4 24.1 + - - +
91B LEU 3.2 11.2 - - - +
92B VAL* 4.3 8.7 - - + +
111B PHE* 4.1 2.9 - - - -
131B PHE 3.7 0.3 - - - +
132B LEU* 3.2 7.9 - - - +
133B LYS* 2.7 67.9 + - + +
135B THR* 3.8 4.9 + - - -
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Residues in contact with PHE 72 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48B VAL* 3.8 27.8 - - + -
71B GLU* 1.3 70.4 - - - +
73B VAL* 1.3 64.7 + - - +
89B VAL* 3.7 22.9 - - + -
90B ASN* 3.4 6.4 - - - -
91B LEU* 2.9 32.1 + - + +
111B PHE* 3.7 22.3 - + + -
114B VAL* 3.6 26.0 - - + -
116B LYS* 3.9 11.9 - - + -
130B TYR* 3.5 38.4 - + + -
131B PHE 3.6 4.5 - - - -
132B LEU* 3.9 23.1 - - + -
149B LEU* 3.9 18.2 - - + -
151B VAL* 5.4 0.2 - - + -
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Residues in contact with VAL 73 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71B GLU* 3.9 20.9 - - + +
72B PHE* 1.3 84.6 - - - +
74B GLY* 1.3 63.0 + - - +
75B GLN* 3.4 28.5 - - - +
87B GLU* 3.8 20.0 - - - +
89B VAL 3.5 3.4 - - - +
90B ASN* 4.0 11.7 - - - +
129B ARG 4.0 0.3 - - - +
130B TYR* 3.1 4.9 - - - +
131B PHE* 2.7 71.6 + - + +
133B LYS* 4.6 8.3 - - + -
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Residues in contact with GLY 74 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73B VAL* 1.3 74.7 - - - +
75B GLN* 1.3 61.5 + - - +
87B GLU* 3.6 1.6 - - - +
88B PHE* 3.0 35.4 + - - -
89B VAL* 3.0 19.5 + - - +
129B ARG 3.5 7.0 - - - -
130B TYR* 3.8 19.5 - - - -
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Residues in contact with GLN 75 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73B VAL* 3.4 15.8 - - + +
74B GLY* 1.3 75.7 - - - +
76B ILE* 1.3 64.8 - - - +
77B GLU* 3.1 27.7 + - + +
85B THR* 3.6 25.4 + - + +
86B HIS 3.3 14.6 - - - +
87B GLU* 3.8 17.0 - - + +
88B PHE* 3.2 6.3 - - - -
127B ARG 4.0 0.5 - - - +
128B LEU* 3.4 4.2 - - - -
129B ARG* 3.1 45.7 + - + +
131B PHE* 3.5 17.9 - - + -
133B LYS* 5.7 0.5 + - - -
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Residues in contact with ILE 76 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75B GLN* 1.3 74.8 - - - +
77B GLU* 1.3 62.7 + - - +
78B LEU* 3.7 24.4 + - + -
84B ASN 3.7 3.6 - - - +
85B THR* 3.6 1.8 - - - -
86B HIS* 2.9 35.8 + - - +
88B PHE* 3.9 12.8 - - + -
118B TYR* 4.6 0.2 - - + -
126B VAL* 4.2 0.7 - - + -
127B ARG 3.3 7.0 - - - +
128B LEU* 3.5 34.1 - - + -
264B VAL* 3.9 9.4 - - + +
265B ASN* 3.6 33.9 - - + +
267B LYS* 4.4 13.5 - - + -
268B PHE* 4.1 15.9 - - + -
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Residues in contact with GLU 77 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75B GLN* 3.1 22.4 + - + +
76B ILE* 1.3 74.9 - - - +
78B LEU* 1.3 60.2 + - - +
80B ASN* 5.5 2.5 - - - +
81B ASP 5.9 1.3 - - - +
84B ASN 4.4 2.7 - - - -
85B THR* 4.2 15.0 - - + +
126B VAL* 3.4 3.8 - - - -
127B ARG* 2.8 59.8 + - + +
129B ARG* 2.9 45.4 + - - +
411B EDO 3.1 17.6 + - - +
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Residues in contact with LEU 78 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76B ILE* 3.7 22.4 - - + +
77B GLU* 1.3 80.8 - - - +
79B PHE* 1.3 85.4 + - + +
80B ASN 3.2 2.4 - - - +
81B ASP* 3.1 20.6 + - - +
84B ASN* 3.7 36.0 + - - +
86B HIS* 4.1 14.4 - - + +
125B ASN 3.4 2.9 - - - +
126B VAL* 4.0 21.5 - - + -
217B THR* 4.1 13.0 - - + -
218B GLY* 5.6 3.8 - - - +
267B LYS* 4.4 19.3 - - + +
268B PHE* 5.1 0.2 - - + -
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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