Contacts of the strand formed by residues 68 - 75 (chain A) in PDB entry 2F1W
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 GLU 68 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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66A ARG* 3.4 19.1 + - - +
67A SER* 1.3 89.3 + - - +
69A ALA* 1.3 66.1 + - - +
92A VAL* 3.9 5.6 - - - +
194A PHE* 3.6 20.8 - - + -
195A VAL 3.1 15.0 - - - +
196A GLN* 3.0 33.1 + - + +
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Residues in contact with ALA 69 (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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66A ARG* 3.3 36.3 - - - +
68A GLU* 1.3 79.6 - - - +
70A THR* 1.3 63.8 + - - +
71A PHE* 4.2 1.1 - - - -
90A CYS* 3.9 8.1 - - - -
92A VAL* 3.5 15.2 - - + +
193A VAL 3.7 1.2 - - - +
194A PHE* 3.4 5.7 - - - -
195A VAL* 2.9 34.1 + - + +
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Residues in contact with THR 70 (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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66A ARG* 5.5 1.1 + - - +
69A ALA* 1.3 74.2 - - - +
71A PHE* 1.3 65.5 + - - +
72A GLN* 3.8 9.4 + - - +
192A GLU* 3.5 36.6 - - + +
193A VAL 3.2 8.1 - - - +
194A PHE* 3.2 27.3 - - + +
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Residues in contact with PHE 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 THR* 1.3 76.9 - - - +
72A GLN* 1.3 74.9 + - - +
87A SER* 3.7 17.5 - - - -
88A PRO 4.6 2.7 - - - -
90A CYS* 3.5 38.8 - - + -
97A TRP* 3.8 32.5 - - + -
98A LYS 4.1 3.6 - - - -
99A ILE* 3.6 33.8 - - + +
119A LEU* 4.2 4.0 - - + -
192A GLU* 3.3 2.8 - - - +
193A VAL* 2.9 56.9 + - + -
195A VAL* 4.4 9.0 - - + -
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Residues in contact with GLN 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 THR* 3.8 17.4 + - - +
71A PHE* 1.3 84.7 - - - +
73A PHE* 1.3 62.7 + - - +
74A THR* 4.3 0.9 - - - +
87A SER* 5.2 1.6 - - - -
88A PRO* 5.5 4.7 - - - +
99A ILE* 4.5 1.8 - - - -
141A ILE* 4.3 10.8 - - + -
190A THR* 3.9 11.9 - - + -
191A PHE 3.1 8.5 - - - +
192A GLU* 2.9 35.8 + - + +
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Residues in contact with PHE 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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72A GLN* 1.3 73.6 - - - +
74A THR* 1.3 73.5 + - - +
75A VAL* 3.7 26.0 - - + -
85A VAL* 3.9 25.8 - - + -
86A LEU 3.6 17.5 - - - -
87A SER* 3.3 42.4 - - - -
88A PRO* 4.4 8.5 - - + -
99A ILE* 3.8 29.2 - - + -
101A VAL* 4.2 4.0 - - + -
190A THR* 3.5 1.0 - - - -
191A PHE* 2.8 39.1 + + - -
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Residues in contact with THR 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 GLN* 5.5 0.9 - - - +
73A PHE* 1.3 83.4 + - - +
75A VAL* 1.3 63.7 + - - +
76A GLU* 3.6 12.5 + - + +
143A TYR* 4.5 0.7 - - - +
188A LYS* 3.9 35.2 - - + -
189A VAL 3.5 4.7 - - - +
190A THR* 2.8 29.1 + - - +
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Residues in contact with VAL 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 PHE* 3.7 34.3 - - + -
74A THR* 1.3 72.1 - - - +
76A GLU* 1.3 71.9 + - - +
78A PHE* 3.8 25.7 - - + +
81A LEU* 4.4 18.8 - - + -
85A VAL* 4.2 13.0 - - + -
101A VAL* 4.3 5.4 - - + -
187A ASP 3.8 0.9 - - - +
188A LYS* 3.4 2.8 - - - -
189A VAL 2.9 33.2 + - - +
191A PHE* 3.9 19.7 - - + -
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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