Contacts of the helix formed by residues 59 - 71 (chain B) in PDB entry 2F4N
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 ASN 59 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55B ILE* 3.4 10.0 - - - +
56B LYS* 2.8 25.8 + - + +
57B PRO 3.2 3.3 + - - +
58B PHE* 1.3 75.0 - - - +
60B ILE* 1.3 60.5 + - - +
61B TYR* 3.2 20.2 + - - +
62B HIS* 3.0 31.2 + - + +
63B GLY 3.2 15.1 + - - -
83B ILE* 3.7 3.4 - - - +
257B TYR* 3.4 38.4 - - - +
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Residues in contact with ILE 60 (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 PHE 3.2 10.2 + - - +
59B ASN* 1.3 71.4 + - - +
61B TYR* 1.3 91.8 + - + +
63B GLY 3.6 0.6 - - - +
64B ALA* 2.6 36.6 + - - +
83B ILE* 3.9 18.2 - - + +
85B PRO* 4.2 11.2 - - + -
109B ASN* 3.3 50.7 - - + +
111B LEU* 3.7 15.5 - - + +
168B ILE* 4.6 9.6 - - + +
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Residues in contact with TYR 61 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59B ASN* 3.2 13.7 + - - +
60B ILE* 1.3 98.0 - - + +
62B HIS* 1.3 65.1 + - - +
64B ALA* 3.2 5.6 + - - +
65B TYR* 2.9 25.6 + - - +
114B TYR* 4.5 8.4 - - - +
168B ILE* 3.6 40.5 - - + +
174B ARG* 4.2 9.9 + - - -
176B ILE* 4.1 10.8 - - - +
257B TYR* 4.1 15.5 - + + -
258B LEU* 3.7 46.1 - - + +
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Residues in contact with HIS 62 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54B GLU 3.6 3.8 - - - -
55B ILE* 3.6 13.4 - - + +
56B LYS* 2.9 40.6 + - + +
59B ASN* 3.0 25.2 + - + +
61B TYR* 1.3 79.4 - - - +
63B GLY* 1.3 63.6 + - - +
65B TYR* 3.1 1.9 + - - +
66B VAL* 3.1 27.0 + - + +
177B HIS* 3.3 23.1 - + - -
257B TYR* 3.4 19.4 - - - +
24C ASN* 2.7 45.1 + - - -
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Residues in contact with GLY 63 (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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18B THR* 5.1 0.6 - - - +
55B ILE* 3.5 24.1 - - - +
59B ASN 3.2 9.4 + - - -
60B ILE 3.7 2.5 - - - -
62B HIS* 1.3 80.3 - - - +
64B ALA* 1.3 61.9 + - - +
66B VAL* 3.2 2.9 + - - +
67B LEU* 3.0 27.4 + - - +
83B ILE* 4.1 5.8 - - - -
111B LEU* 3.6 15.0 - - - -
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Residues in contact with ALA 64 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60B ILE 2.6 22.3 + - - +
61B TYR 3.5 4.9 - - - +
63B GLY* 1.3 72.6 - - - +
65B TYR* 1.3 58.3 + - - +
67B LEU* 3.3 3.4 + - - +
68B LEU* 3.1 28.1 + - - +
110B GLY 4.5 0.2 - - - +
111B LEU* 3.2 26.1 - - - +
114B TYR* 3.7 26.4 - - + +
115B VAL 5.2 1.2 + - - -
168B ILE* 3.9 15.5 - - + -
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Residues in contact with TYR 65 (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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61B TYR 2.9 17.4 + - - +
62B HIS 3.1 4.7 + - - +
64B ALA* 1.3 75.4 - - - +
66B VAL* 1.3 67.2 + - + +
68B LEU* 3.5 8.7 + - + +
69B THR* 3.0 40.8 + - + -
114B TYR* 4.2 8.0 - + + -
176B ILE* 3.9 24.2 - - + +
177B HIS* 3.4 42.8 - + + -
185B ILE* 3.5 39.8 - - + +
235B ASN* 3.8 2.8 + - - -
237B GLU* 2.8 35.6 + - + +
239B PHE* 4.2 12.1 - + - -
25C GLU* 5.2 8.1 - - + -
26C GLY 6.0 0.7 - - - -
27C TYR* 6.4 0.2 - + - -
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Residues in contact with VAL 66 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18B THR* 4.9 3.6 - - + -
51B ILE* 3.6 22.0 - - + -
52B SER* 4.3 9.2 - - - -
55B ILE* 3.6 23.6 - - + -
62B HIS* 3.1 11.5 + - + +
63B GLY 3.2 5.6 + - - +
65B TYR* 1.3 77.9 - - + +
67B LEU* 1.3 65.1 + - - +
69B THR* 3.2 3.8 + - - -
70B ALA* 3.1 21.3 + - - +
23C THR 5.3 0.2 - - - +
24C ASN 3.6 24.7 - - - +
25C GLU* 4.0 12.8 - - - +
26C GLY* 3.6 22.7 - - - +
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Residues in contact with LEU 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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18B THR* 3.8 31.6 - - + +
51B ILE* 4.4 5.8 - - + -
63B GLY 3.0 13.6 + - - +
64B ALA 3.7 4.0 - - - +
66B VAL* 1.3 77.6 - - - +
68B LEU* 1.3 60.9 + - - +
70B ALA* 4.7 1.3 - - - +
71B ILE* 3.1 56.8 + - + +
72B PRO* 3.8 0.2 - - - +
79B HIS* 5.5 2.5 - - + -
80B VAL 5.6 0.4 - - - +
81B ALA* 3.8 11.2 - - + -
111B LEU* 3.8 31.6 - - + +
112B PHE* 3.5 30.1 - - + -
115B VAL* 3.9 9.8 - - + +
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Residues in contact with LEU 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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64B ALA 3.1 17.0 + - - +
65B TYR* 3.7 12.1 - - + +
66B VAL 3.3 0.2 - - - -
67B LEU* 1.3 76.5 - - - +
69B THR* 1.3 62.5 + - - +
72B PRO* 3.5 14.7 - - + +
73B TYR* 5.4 1.6 - - - -
114B TYR* 3.7 38.6 - - + +
115B VAL* 4.4 8.2 - - - +
118B LYS* 4.3 32.5 - - + -
237B GLU* 5.5 5.6 - - + -
239B PHE* 4.1 29.4 - - + -
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Residues in contact with THR 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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65B TYR* 3.0 21.5 + - - -
66B VAL 3.2 8.9 + - - -
67B LEU 3.2 0.4 - - - -
68B LEU* 1.3 81.2 - - - +
70B ALA* 1.3 58.1 + - - +
73B TYR* 3.5 24.1 - - - -
237B GLU* 3.5 40.3 - - + +
25C GLU* 5.9 0.2 - - + -
26C GLY* 3.7 29.6 + - - +
27C TYR* 4.0 12.8 - - + -
30C ALA* 3.5 6.6 - - + +
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Residues in contact with ALA 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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51B ILE* 3.9 26.2 - - + -
66B VAL 3.1 13.8 + - - +
67B LEU 4.5 0.2 - - - +
69B THR* 1.3 78.6 - - - +
71B ILE* 1.3 66.9 + - - +
72B PRO 3.5 1.1 - - - -
73B TYR* 3.2 17.5 + - - +
74B PHE* 3.3 13.6 - - + -
26C GLY 3.5 17.3 - - - +
29C GLY* 3.8 6.7 - - - -
30C ALA* 3.6 14.2 - - - +
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Residues in contact with ILE 71 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51B ILE* 4.3 8.7 - - + -
67B LEU* 3.1 38.2 + - + +
70B ALA* 1.3 73.6 - - - +
72B PRO* 1.3 61.4 - - + +
73B TYR 2.7 12.0 + - - -
74B PHE* 2.8 28.0 + - - +
79B HIS* 3.7 47.1 - - + +
102B TYR* 4.1 3.1 - - + -
104B LEU* 4.1 8.5 - - + -
112B PHE* 4.7 1.6 - - + -
115B VAL* 3.6 22.9 - - + -
119B LEU* 3.8 24.5 - - + -
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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