Contacts of the strand formed by residues 70 - 77 (chain A) in PDB entry 4FOV
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 GLN 70 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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65A LEU* 3.7 25.8 - - + +
66A SER 3.2 10.1 + - - +
67A GLY 3.1 22.4 + - - +
68A GLU* 3.6 12.0 - - - +
69A SER* 1.3 88.6 + - - +
71A THR* 1.3 61.0 + - - +
72A VAL* 5.6 0.4 - - - -
148A PHE* 4.0 1.3 - - - +
149A VAL* 3.8 0.5 - - - +
150A SER* 2.9 38.1 + - - +
176A PRO* 5.1 0.3 - - - +
177A ILE* 3.9 34.4 + - + +
178A SER* 4.1 8.1 + - - -
210A LEU* 5.2 3.1 - - + -
211A PHE 3.2 14.1 - - - +
212A ASN* 3.1 19.1 + - - +
213A LYS 3.2 7.1 - - - +
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Residues in contact with THR 71 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70A GLN* 1.3 74.1 + - - +
72A VAL* 1.3 69.5 + - - +
73A VAL* 4.2 6.5 - - + -
147A VAL* 4.0 13.5 - - + -
148A PHE 3.3 9.6 - - - +
149A VAL* 3.8 5.9 - - + +
210A LEU* 3.2 7.6 - - - +
211A PHE* 2.9 43.4 + - + +
213A LYS 2.8 18.8 + - - -
214A ALA* 3.7 1.4 - - - -
215A ILE* 3.2 45.0 + - + +
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Residues in contact with VAL 72 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70A GLN 5.6 0.4 - - - -
71A THR* 1.3 76.2 - - - +
73A VAL* 1.3 69.5 + - - +
74A MET* 4.6 5.6 - - + -
88A PHE* 4.6 10.1 - - + -
102A PHE* 4.9 0.4 - - + -
104A ILE* 4.0 30.3 - - + -
146A LEU* 3.5 2.6 - - + +
147A VAL* 3.3 5.9 - - - +
148A PHE* 2.9 48.0 + - + +
177A ILE* 4.8 10.1 - - + -
208A ILE* 4.2 22.0 - - + -
209A SER 3.5 7.0 - - - +
210A LEU* 3.9 24.5 - - + -
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Residues in contact with VAL 73 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71A THR* 4.2 5.1 - - + -
72A VAL* 1.3 78.7 - - - +
74A MET* 1.3 66.8 + - - +
75A LYS* 5.5 2.5 - - + -
145A THR* 5.2 4.5 - - + -
146A LEU 3.3 6.1 - - - +
147A VAL* 4.2 12.1 - - + -
207A GLU* 3.8 18.8 - - - +
208A ILE* 3.2 5.2 - - - +
209A SER* 2.8 44.2 + - - +
211A PHE* 3.9 19.1 - - + -
215A ILE* 5.0 0.9 - - + -
223A ILE* 3.9 38.6 - - + -
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Residues in contact with MET 74 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72A VAL* 4.6 2.7 - - + -
73A VAL* 1.3 77.7 - - - +
75A LYS* 1.3 62.5 + - - +
76A PHE* 4.0 11.7 + - + -
87A LEU* 3.5 38.4 - - + -
88A PHE* 4.5 5.4 - - + -
104A ILE* 4.0 23.3 - - + -
144A ASN 3.5 2.4 - - - +
145A THR 3.7 0.2 - - - -
146A LEU* 2.8 58.6 + - + +
205A ILE* 3.7 39.5 - - + -
207A GLU 3.3 3.4 - - - +
208A ILE* 3.9 18.6 - - + -
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Residues in contact with LYS 75 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73A VAL* 5.2 2.4 - - + +
74A MET* 1.3 73.2 - - - +
76A PHE* 1.3 55.2 + - - +
143A GLU* 3.2 34.7 + - - +
144A ASN 3.2 3.8 - - - +
145A THR* 2.7 40.7 + - + +
205A ILE* 3.5 2.1 - - - +
206A ASP* 2.7 31.8 + - + -
207A GLU* 2.8 51.7 + - + +
223A ILE* 5.1 3.4 - - - -
224A PRO* 3.1 34.2 + - - +
225A LEU* 4.0 0.6 - - - +
226A SER* 3.7 11.3 + - - -
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Residues in contact with PHE 76 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74A MET* 4.1 16.6 - - + -
75A LYS* 1.3 74.6 - - - +
77A LYS* 1.3 72.3 + - - +
78A ALA* 4.3 5.2 - - + -
87A LEU* 3.6 38.6 - - + -
106A MET* 3.9 17.3 - - + -
112A ILE* 4.4 3.1 - - + -
133A LEU* 3.8 26.7 - - + -
143A GLU* 4.3 1.2 - - - +
144A ASN* 2.8 59.2 + - + +
146A LEU* 4.2 19.1 - - + -
204A SER 3.1 14.8 - - - +
205A ILE* 4.0 15.5 - - + -
206A ASP* 4.3 2.0 - - - +
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Residues in contact with LYS 77 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76A PHE* 1.3 82.2 - - - +
78A ALA* 1.3 64.1 + - - +
79A ASP* 5.9 0.2 - - - +
87A LEU* 5.9 0.5 - - - +
140A GLN* 5.7 4.6 - - - +
141A ALA* 3.9 33.9 + - + +
142A VAL 3.4 20.6 - - - +
143A GLU* 4.0 13.6 + - - -
144A ASN* 4.7 0.2 - - - +
203A GLY* 3.4 0.9 - - - -
204A SER* 2.8 45.0 + - - +
206A ASP* 3.3 24.7 + - - +
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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