Contacts of the strand formed by residues 65 - 73 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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63B LEU 3.3 1.5 - - - +
64B PRO* 1.3 84.5 - - + +
66B SER* 1.3 69.2 - - - +
67B CYS* 4.4 4.0 - - - -
107B ILE 3.9 0.2 - - - +
108B ASN* 3.2 3.8 - - - -
109B ALA* 2.7 40.0 + - + +
111B SER* 3.9 13.0 - - - +
112B LEU* 3.8 46.2 - - + +
115B VAL* 3.9 18.3 - - + +
132B VAL* 5.0 5.2 - - + -
112G LEU* 5.1 12.1 - - + -
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Residues in contact with SER 66 (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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58B GLN* 5.6 0.7 - - - +
63B LEU 5.1 1.7 + - - -
64B PRO 4.2 2.6 + - - -
65B VAL* 1.3 74.9 - - - +
67B CYS* 1.3 69.1 - - - +
106B LYS* 3.9 6.6 + - - -
107B ILE 3.1 7.0 - - - -
108B ASN* 2.8 26.5 + - - -
132B VAL* 4.0 1.2 - - - +
133B ILE* 3.0 51.3 + - - +
112G LEU* 6.1 0.2 - - - +
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Residues in contact with CYS 67 (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 VAL* 4.4 3.4 - - - -
66B SER* 1.3 80.8 - - - +
68B ILE* 1.3 59.2 + - - +
69B VAL* 4.2 1.6 - - + -
106B LYS* 3.3 6.4 - - - +
107B ILE* 3.0 41.8 + - + +
115B VAL* 3.9 28.3 - - - -
130B THR* 3.8 28.3 - - + -
131B HIS 3.1 9.6 - - - +
132B VAL* 4.1 17.3 - - - -
133B ILE* 3.9 7.6 - - - -
134G PHE* 5.8 0.2 - - - -
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Residues in contact with ILE 68 (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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68A ILE* 6.3 0.2 - - + -
93A PHE* 5.1 2.2 - - + -
95A TYR* 3.9 18.8 - - + -
97A ILE* 4.1 11.9 - - + -
104A MET* 4.1 20.9 - - + -
67B CYS* 1.3 73.4 - - - +
69B VAL* 1.3 64.5 + - - +
93B PHE* 4.1 10.8 - - + -
104B MET* 3.7 28.0 - - + -
105B LEU 3.2 7.2 - - - +
106B LYS* 3.9 20.6 - - + -
131B HIS* 2.8 44.7 + - + +
133B ILE* 3.6 28.7 - - + +
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Residues in contact with VAL 69 (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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67B CYS* 4.2 15.5 - - + -
68B ILE* 1.3 79.3 - - - +
70B GLU* 1.3 67.0 + - - +
71B ALA* 4.8 0.9 - - + +
103B TYR 3.6 0.7 - - - +
104B MET* 3.4 4.9 - - - -
105B LEU* 2.8 61.7 + - + +
107B ILE* 4.3 7.2 - - + -
118B PHE* 4.1 22.2 - - + -
128B THR* 3.7 34.8 - - + -
129B VAL 3.5 4.7 - - - +
130B THR* 4.3 12.1 - - + +
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Residues in contact with GLU 70 (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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70A GLU* 4.7 8.4 - - - +
104A MET* 4.4 2.3 - - - +
131A HIS* 5.9 0.9 - - - -
68B ILE 4.3 0.2 - - - -
69B VAL* 1.3 73.6 - - - +
71B ALA* 1.3 60.1 + - - +
72B THR* 5.1 1.7 - - + +
101B ALA* 3.8 21.8 - - + +
103B TYR 3.3 5.2 - - - -
104B MET* 3.5 32.8 - - + +
127B GLN 3.6 0.3 - - - +
128B THR* 3.1 7.1 - - - -
129B VAL* 3.0 47.3 + - + +
131B HIS* 2.8 30.2 + - - +
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Residues in contact with ALA 71 (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 VAL* 3.9 2.2 + - + -
70B GLU* 1.3 71.8 - - - +
72B THR* 1.3 62.9 - - - +
73B VAL 4.2 0.4 - - - +
81B PHE* 3.7 29.8 - - + -
101B ALA* 3.5 1.6 - - - +
102B CYS* 2.8 25.2 + - - +
103B TYR* 2.8 23.9 + - + -
105B LEU* 5.0 7.0 - - + -
126B ALA* 3.8 15.3 - - + -
127B GLN 3.2 3.6 - - - +
128B THR* 4.6 6.5 - - + +
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Residues in contact with THR 72 (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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70B GLU* 5.1 2.5 - - + +
71B ALA* 1.3 77.6 - - - +
73B VAL* 1.3 69.2 + - - +
100B ALA 4.4 6.9 + - - +
101B ALA* 3.8 22.0 - - + -
102B CYS* 3.8 11.5 - - - -
126B ALA* 3.1 2.5 - - - -
127B GLN* 2.7 67.5 + - + +
129B VAL* 6.0 5.2 - - + -
127H GLN* 5.9 0.7 + - - -
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Residues in contact with VAL 73 (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 THR* 1.3 78.1 + - - +
74B LYS* 1.3 63.0 + - - +
75B ASN 4.2 0.3 + - - -
76B ALA* 3.9 7.3 + - - -
77B ASP 3.4 38.8 - - - +
78B TYR* 3.8 34.9 + - + +
81B PHE* 3.7 35.9 - - + -
102B CYS* 3.3 11.0 - - + -
103B TYR* 3.9 12.8 - - + -
125B TYR 3.8 3.6 - - - +
126B ALA* 4.2 0.9 - - + +
74H LYS* 5.4 4.9 + - - -
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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