Contacts of the strand formed by residues 86 - 96 (chain B) in PDB entry 5F0P
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 HIS 86 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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75B GLN* 3.3 3.7 - - - -
76B ILE* 3.0 35.7 + - + +
84B ASN 3.4 3.5 + - - +
85B THR* 1.3 73.0 - - - +
87B GLU* 1.3 83.4 + - - +
88B PHE* 3.5 10.8 + + + +
265B ASN* 3.1 30.4 + - - -
267B LYS* 3.4 26.8 + - + -
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Residues in contact with GLU 87 (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* 5.1 0.3 - - - +
73B VAL* 3.7 19.0 - - + +
74B GLY 3.6 7.6 - - - +
75B GLN* 3.7 21.7 - - - +
85B THR* 4.2 3.0 + - + -
86B HIS* 1.3 88.6 + - - +
88B PHE* 1.3 60.2 + - - +
89B VAL 4.3 7.2 - - - +
90B ASN* 2.7 37.0 + - + +
133B LYS* 4.4 12.3 + - - -
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Residues in contact with PHE 88 (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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74B GLY* 3.0 25.2 + - - -
75B GLN* 3.2 31.6 - - - -
76B ILE* 4.0 12.1 - - + -
86B HIS* 4.0 8.7 - - + +
87B GLU* 1.3 74.1 - - - +
89B VAL* 1.3 75.2 + - + +
117B PRO* 3.9 10.7 - - + +
118B TYR* 3.7 22.9 - + + -
128B LEU* 3.7 20.4 - - + -
130B TYR* 3.4 42.4 - + - -
265B ASN* 4.1 21.8 - - - +
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Residues in contact with VAL 89 (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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72B PHE* 3.7 35.4 - - + +
73B VAL* 3.4 6.6 - - - +
74B GLY 3.0 31.3 + - - +
87B GLU* 4.3 2.9 - - - +
88B PHE* 1.3 101.9 - - + +
90B ASN* 1.3 64.0 + - - +
91B LEU* 4.7 10.3 - - + -
114B VAL* 4.8 0.9 - - + -
115B GLU* 3.6 26.9 - - + +
116B LYS* 5.2 0.2 - - - -
117B PRO* 4.1 10.3 - - + -
130B TYR* 5.2 0.4 - - + -
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Residues in contact with ASN 90 (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* 3.0 28.3 + - - +
72B PHE 3.4 3.6 - - - -
73B VAL* 3.7 10.5 - - - +
87B GLU* 2.7 35.3 + - + +
89B VAL* 1.3 75.2 - - - +
91B LEU* 1.3 74.6 + - - +
92B VAL* 3.6 18.1 - - - +
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Residues in contact with LEU 91 (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* 3.1 9.2 - - - +
72B PHE* 3.0 34.5 + - + +
89B VAL* 4.7 8.3 - - + -
90B ASN* 1.3 84.6 + - - +
92B VAL* 1.3 64.5 + - - +
111B PHE* 3.5 31.1 - - + -
112B MSE 5.6 2.5 - - - +
114B VAL* 3.9 36.8 - - + -
115B GLU 5.6 0.7 - - - +
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Residues in contact with VAL 92 (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* 3.9 22.2 - - - -
70B ILE 3.6 5.2 - - - +
71B GLU* 4.4 7.0 - - + +
90B ASN* 3.6 16.8 - - - +
91B LEU* 1.3 80.0 - - - +
93B LYS* 1.3 80.2 + - - +
94B GLU* 3.7 23.8 - - + +
111B PHE* 4.1 1.7 - - - -
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Residues in contact with LYS 93 (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* 3.3 1.2 - - - -
70B ILE* 2.8 54.3 + - + +
92B VAL* 1.3 83.6 + - - +
94B GLU* 1.3 67.1 + - - +
95B LEU* 3.5 5.9 + - + -
109B PHE* 4.8 7.0 - - + -
110B GLU 3.1 28.4 + - - +
111B PHE* 3.7 24.0 - - + +
112B MSE 6.0 2.4 - - - +
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Residues in contact with GLU 94 (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 3.8 3.5 - - - +
69B ARG* 3.5 7.8 - - - +
92B VAL* 3.7 17.8 - - + +
93B LYS* 1.3 73.6 - - - +
95B LEU* 1.3 63.0 + - - +
96B ALA 3.7 6.1 - - - +
405B EDO 2.8 44.6 + - - -
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Residues in contact with LEU 95 (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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52B VAL* 3.6 32.8 - - + -
68B ILE* 2.8 28.3 + - + +
69B ARG 4.0 8.7 - - - +
70B ILE* 3.8 26.5 - - + +
93B LYS* 3.9 10.5 - - + +
94B GLU* 1.3 78.7 - - - +
96B ALA* 1.3 60.1 + - - +
107B TYR* 3.5 35.7 - - + -
108B ASP 3.5 24.7 - - - +
109B PHE* 4.3 4.3 - - + -
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Residues in contact with ALA 96 (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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65B HIS* 4.3 3.1 - - + -
67B GLY* 3.4 3.6 - - - -
68B ILE* 3.1 43.4 + - + +
94B GLU* 3.7 6.7 - - - +
95B LEU* 1.3 81.2 - - - +
97B LEU* 1.3 68.8 + - - +
107B TYR* 3.9 22.4 - - + +
405B EDO 5.4 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