Contacts of the strand formed by residues 71 - 77 (chain I) in PDB entry 5FUR
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 ARG 71 (chain I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70I CYS* 1.4 71.5 - - - +
72I ILE* 1.3 66.9 + - - +
73I TYR* 5.2 9.6 - - - +
150I PHE* 3.6 1.9 - - - -
151I SER* 2.8 60.9 + - - +
152I LEU 5.4 0.2 - - - +
153I ASP* 3.6 12.4 + - - +
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Residues in contact with ILE 72 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67I SER* 5.2 0.7 - - - +
70I CYS* 3.2 21.8 + - + +
71I ARG* 1.3 86.4 + - - +
73I TYR* 1.3 65.8 + - - +
74I ARG* 3.9 9.6 - - - +
75I VAL* 4.1 22.7 - - + -
84I PHE* 5.0 8.7 - - + -
86I TYR* 5.3 5.8 - - + -
126I LEU* 4.2 17.9 - - + -
148I ILE* 4.4 4.3 - - + -
149I ASN 3.8 8.1 - - - +
150I PHE* 4.4 4.9 - - + -
191I PRO* 3.7 30.5 - - + -
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Residues in contact with TYR 73 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71I ARG* 4.0 12.4 + - + +
72I ILE* 1.3 77.2 - - - +
74I ARG* 1.3 99.7 + - + +
81I GLU* 5.6 1.2 - - - +
149I ASN* 2.9 43.9 + - - +
150I PHE* 4.7 1.5 - - - +
151I SER* 6.0 2.0 - - - -
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Residues in contact with ARG 74 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72I ILE* 3.8 2.7 - - - +
73I TYR* 1.3 116.8 + - + +
75I VAL* 1.3 77.3 + - - +
76I ARG* 4.0 15.7 - - + +
81I GLU* 2.9 46.9 + - + +
147I HIS 3.7 2.3 - - - +
148I ILE* 3.7 3.1 - - - +
149I ASN* 3.0 30.8 + - + +
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Residues in contact with VAL 75 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72I ILE* 4.1 14.8 - - + +
74I ARG* 1.3 79.2 - - - +
76I ARG* 1.3 62.2 + - - +
77I ILE* 4.8 0.9 - - + -
81I GLU* 3.5 10.0 + - - +
82I ALA* 3.1 35.2 + - + +
84I PHE* 3.5 39.9 - - + -
128I ILE* 2.5 44.2 - - + -
146I ILE* 4.7 3.8 - - + -
147I HIS 3.9 2.5 - - - -
148I ILE* 4.6 11.4 - - + +
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Residues in contact with ARG 76 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48I PHE* 6.1 2.4 - - - -
50I GLU* 5.5 1.8 + - - -
74I ARG* 4.8 17.5 - - + +
75I VAL* 1.3 76.5 - - - +
77I ILE* 1.3 62.5 + - - +
79I ASP* 2.7 50.4 + - - +
80I LEU 3.4 17.0 - - - +
81I GLU* 4.8 0.7 - - - +
146I ILE* 4.7 0.2 - - - +
147I HIS* 3.0 83.5 + - - +
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Residues in contact with ILE 77 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75I VAL 4.2 0.8 + - - -
76I ARG* 1.3 76.5 - - - +
78I ASN* 1.3 85.4 + - - +
79I ASP 3.2 1.8 - - - -
80I LEU* 3.0 21.2 + - - +
82I ALA* 4.0 8.6 - - + +
128I ILE* 3.8 31.2 - - + -
129I LYS 3.8 22.2 - - - +
130I VAL* 4.1 13.2 - - + -
131I PRO* 3.7 35.5 - - + +
144I LEU* 5.3 11.2 - - + -
145I LYS 4.6 6.5 - - - +
146I ILE* 4.5 16.2 - - + -
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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