Contacts of the helix formed by residues 61 - 72 (chain B) in PDB entry 4F2N
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 LYS 61 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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203A ASN* 3.6 39.5 - - + +
53B ARG* 4.6 13.6 - - - +
56B GLU* 4.7 15.0 + - - -
57B LEU* 3.0 38.0 + - + +
60B SER* 1.3 87.5 + - - +
62B HIS* 1.3 66.2 + - - +
63B HIS 3.6 0.2 - - - -
64B SER* 4.0 0.3 - - - -
65B ALA* 3.1 25.3 + - - +
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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
----------------------------------------------------------
194A GLU* 3.8 8.5 + - - -
197A TYR* 6.0 0.4 - - - -
198A TYR* 2.8 31.6 + + - -
203A ASN* 3.4 25.4 - - + +
57B LEU 3.0 28.3 + - - -
58B HIS* 3.3 19.7 - - + +
61B LYS* 1.3 73.8 - - - +
63B HIS* 1.3 68.1 + - - +
65B ALA* 3.2 13.5 + - - +
66B TYR* 3.1 28.3 + - + -
108B HIS* 5.0 0.2 - - - +
195B HIS* 3.4 43.3 + + + +
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Residues in contact with HIS 63 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35B LEU* 3.5 7.9 - - + +
36B PRO* 3.5 25.4 - - + -
58B HIS 2.9 16.7 + - - +
59B TYR* 3.4 14.1 - - - +
61B LYS 3.6 0.2 - - - -
62B HIS* 1.3 72.8 - - - +
64B SER* 1.3 64.3 + - - +
66B TYR* 3.1 19.6 + - + +
67B VAL* 3.1 12.1 + - + +
105B HIS* 3.0 39.9 + - - -
108B HIS* 3.4 29.0 - + + +
109B SER* 3.5 11.2 - - - -
112B TRP* 2.9 23.8 + - - +
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Residues in contact with SER 64 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35B LEU* 3.7 22.8 - - - +
59B TYR 3.1 6.7 + - - -
60B SER 3.1 29.7 + - - -
61B LYS 3.7 0.9 + - - -
62B HIS 3.3 0.4 - - - -
63B HIS* 1.3 79.1 - - - +
65B ALA* 1.3 54.8 + - - +
67B VAL* 3.3 3.6 + - - +
68B ASP* 3.0 43.6 + - - +
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Residues in contact with ALA 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 LYS 3.1 19.3 + - - +
62B HIS* 3.6 6.1 - - - +
63B HIS 3.2 0.2 - - - -
64B SER* 1.3 75.7 - - - +
66B TYR* 1.3 59.5 + - + +
68B ASP* 3.8 7.1 - - - +
69B LYS* 3.0 30.5 + - - +
101B GLN* 4.5 0.9 - - - -
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Residues in contact with TYR 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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152A PHE* 4.1 15.0 - + - -
62B HIS* 3.1 33.4 + - + -
63B HIS* 3.1 11.5 + + - +
65B ALA* 1.3 75.0 - - + +
67B VAL* 1.3 66.3 + - - +
70B LEU* 3.0 27.4 + - - +
101B GLN* 3.3 38.8 - - - +
104B GLN* 3.1 45.4 + - + -
105B HIS* 4.4 9.9 - - - +
108B HIS* 3.6 25.8 - + - -
193B TRP* 3.7 20.3 - - - -
195B HIS* 4.5 4.0 - + - -
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Residues in contact with VAL 67 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33B ALA* 3.7 30.7 - - - +
34B GLU* 3.9 0.7 - - - -
35B LEU* 3.8 27.1 - - + +
63B HIS* 3.1 18.8 + - + +
64B SER* 3.6 9.0 - - - +
66B TYR* 1.3 75.6 - - - +
68B ASP* 1.3 71.7 + - - +
70B LEU* 3.8 2.2 - - - +
71B ASN* 3.1 32.8 + - - +
105B HIS* 3.5 36.1 - - + +
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Residues in contact with ASP 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 SER* 3.0 31.4 + - - +
65B ALA* 3.8 6.6 - - - +
67B VAL* 1.3 88.3 - - - +
69B LYS* 1.3 62.9 + - - +
71B ASN* 3.4 13.4 + - - +
72B THR* 3.6 16.0 + - - +
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Residues in contact with LYS 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 ALA 3.0 11.7 + - - +
68B ASP* 1.3 77.2 - - - +
70B LEU* 1.3 61.6 + - - +
72B THR* 2.6 38.0 + - + +
73B LEU* 3.5 20.1 - - + +
97B VAL* 4.4 13.7 - - - -
101B GLN* 3.2 37.7 - - + +
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Residues in contact with LEU 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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31B TYR* 3.6 10.9 + - + -
33B ALA* 3.8 20.9 - - + -
66B TYR 3.0 18.1 + - - +
67B VAL 3.8 3.6 - - - +
69B LYS* 1.3 77.7 - - - +
71B ASN* 1.3 56.6 + - - +
73B LEU* 2.9 20.8 + - - -
74B GLY 3.0 12.8 + - - -
82B ILE* 4.0 18.6 - - + -
85B ILE* 4.5 10.5 - - + -
98B MET* 4.1 22.0 - - + +
101B GLN* 4.0 9.6 - - + +
102B ALA* 3.9 39.5 - - + +
105B HIS* 4.1 11.2 - - + -
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Residues in contact with ASN 71 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31B TYR* 3.3 23.7 + - - -
32B PRO* 3.6 9.3 - - - +
33B ALA* 2.8 46.9 + - - +
67B VAL* 3.1 24.7 + - - +
68B ASP* 3.8 8.5 + - - +
69B LYS 3.2 0.4 - - - -
70B LEU* 1.3 73.9 - - - +
72B THR* 1.3 58.7 + - + +
73B LEU 3.3 0.2 - - - -
75B LYS 5.5 0.3 + - - -
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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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68B ASP 3.6 13.9 - - - +
69B LYS* 2.6 33.9 + - + +
71B ASN* 1.3 77.8 - - - +
73B LEU* 1.3 68.5 + - - +
75B LYS 5.5 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