Contacts of the strand formed by residues 65 - 73 (chain F) in PDB entry 2CFX
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 VAL 65 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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112C LEU* 5.3 11.9 - - + -
63F LEU 4.2 1.1 - - - +
64F PRO* 1.3 85.4 - - + +
66F SER* 1.3 69.1 + - - +
67F CYS* 4.5 3.1 - - - -
108F ASN* 3.3 4.0 - - - +
109F ALA* 2.6 40.8 + - - +
111F SER* 3.8 28.5 - - - +
112F LEU* 3.8 27.4 - - + +
115F VAL* 3.7 25.6 - - + -
132F VAL* 4.8 5.6 - - + -
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Residues in contact with SER 66 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112C LEU* 6.1 0.4 - - - +
58F GLN* 5.7 0.3 - - - +
63F LEU 5.2 0.9 + - - -
64F PRO 4.2 1.6 + - - -
65F VAL* 1.3 71.9 - - - +
67F CYS* 1.3 69.0 + - - +
106F LYS* 3.8 4.8 + - - -
107F ILE 3.3 5.4 - - - -
108F ASN* 2.6 28.0 + - - -
115F VAL* 6.1 0.2 - - - -
132F VAL* 3.8 3.5 - - - +
133F ILE* 2.9 53.2 + - - +
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Residues in contact with CYS 67 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65F VAL* 4.5 2.9 - - - -
66F SER* 1.3 80.1 - - - +
68F ILE* 1.3 65.8 + - - +
69F VAL* 3.9 4.2 + - + -
105F LEU 3.8 0.2 - - - +
106F LYS* 3.3 5.0 - - - +
107F ILE* 3.0 42.6 + - + +
112F LEU* 5.8 0.2 - - - -
115F VAL* 3.7 38.1 - - - -
130F THR* 3.8 20.9 - - + -
131F HIS 3.3 9.0 - - - +
132F VAL* 4.1 15.5 - - - -
133F ILE* 4.0 2.2 - - - -
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Residues in contact with ILE 68 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93E PHE* 5.4 0.9 - - + -
95E TYR* 3.9 15.9 - - + -
97E ILE* 4.2 15.5 - - + -
104E MET* 4.0 23.6 - - + -
67F CYS* 1.3 71.7 - - - +
69F VAL* 1.3 64.5 + - - +
93F PHE* 4.1 9.6 - - + -
104F MET* 3.7 33.4 - - + -
105F LEU 3.2 5.2 - - - +
106F LYS* 3.8 21.8 - - + -
131F HIS* 2.8 47.0 + - + +
133F ILE* 3.7 23.9 - - + +
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Residues in contact with VAL 69 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67F CYS* 4.2 18.6 - - + +
68F ILE* 1.3 81.5 - - - +
70F GLU* 1.3 64.9 + - - +
71F ALA* 3.8 1.7 + - + +
103F TYR 3.7 0.5 - - - +
104F MET* 3.5 2.4 - - - -
105F LEU* 2.6 62.9 + - + +
107F ILE* 4.3 4.3 - - + -
118F PHE* 3.9 23.6 - - + -
128F THR* 3.8 33.4 - - + -
129F VAL 3.4 6.7 - - - +
130F THR* 4.2 11.7 - - + +
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Residues in contact with GLU 70 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70E GLU* 4.1 17.6 - - - +
104E MET* 4.1 5.4 - - - +
131E HIS* 6.1 0.9 - - - -
69F VAL* 1.3 73.7 - - - +
71F ALA* 1.3 59.5 + - - +
72F THR* 5.2 1.5 - - + +
101F ALA* 3.9 20.8 - - + +
103F TYR 3.3 9.2 - - - +
104F MET* 3.6 20.2 - - - +
127F GLN 3.6 0.3 - - - +
128F THR* 3.1 8.3 - - - -
129F VAL* 2.9 48.7 + - + +
131F HIS* 2.7 35.7 + - - +
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Residues in contact with ALA 71 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69F VAL* 3.8 2.0 + - + +
70F GLU* 1.3 74.8 - - - +
72F THR* 1.3 61.5 + - - +
73F VAL* 4.2 0.7 - - + -
81F PHE* 3.9 34.1 - - + -
101F ALA* 3.7 0.5 - - - +
102F CYS* 2.8 25.2 + - - +
103F TYR* 2.8 24.3 + - + +
105F LEU* 5.0 7.6 - - + -
126F ALA* 4.2 5.2 - - + -
127F GLN 3.4 3.8 - - - -
128F THR* 4.5 7.4 - - + -
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Residues in contact with THR 72 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70F GLU* 5.2 2.0 - - + +
71F ALA* 1.3 77.4 - - - +
73F VAL* 1.3 67.4 + - - +
74F LYS* 3.5 0.7 + - - +
100F ALA 4.4 6.7 + - - +
101F ALA* 3.8 20.9 - - + +
102F CYS* 3.9 14.1 - - - -
126F ALA* 3.2 2.1 - - - +
127F GLN* 2.7 66.4 + - + +
129F VAL* 6.0 5.4 - - + -
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Residues in contact with VAL 73 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74D LYS* 5.6 3.3 + - - -
72F THR* 1.3 75.3 + - - +
74F LYS* 1.3 63.2 + - - +
76F ALA* 4.0 5.8 + - - -
77F ASP 3.3 39.0 - - - +
78F TYR* 3.8 35.6 + - + +
81F PHE* 3.7 35.2 - - + -
102F CYS* 3.3 11.6 - - + -
103F TYR* 4.0 10.5 - - + -
125F TYR 3.8 4.7 - - - +
126F ALA* 4.2 0.7 - - - -
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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