Contacts of the helix formed by residues 61 - 74 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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203C ASN* 3.6 39.7 - - + +
53D ARG* 5.5 8.1 - - - +
56D GLU* 4.3 7.6 - - + +
57D LEU* 3.1 28.3 + - + +
60D SER* 1.3 90.9 - - - +
62D HIS* 1.3 66.4 + - - +
63D HIS 3.6 0.4 - - - -
64D SER 4.1 0.2 - - - -
65D ALA* 3.1 25.3 + - - +
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Residues in contact with HIS 62 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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194C GLU* 3.6 7.6 - - - -
198C TYR* 2.6 33.5 + + - -
203C ASN* 3.4 26.4 - - + +
57D LEU 3.0 28.3 + - - -
58D HIS* 3.3 20.9 - - + +
61D LYS* 1.3 75.9 - - - +
63D HIS* 1.3 66.7 + - - +
65D ALA* 3.4 9.7 + - - +
66D TYR* 3.1 28.3 + - + -
195D HIS* 3.4 43.9 + + + +
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Residues in contact with HIS 63 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35D LEU* 3.5 8.9 - - + +
36D PRO* 3.4 20.0 - - + -
58D HIS 2.9 16.8 + - - +
59D TYR* 3.4 14.1 - - - +
62D HIS* 1.3 73.0 - - - +
64D SER* 1.3 63.5 + - - +
66D TYR* 3.0 19.8 + - + +
67D VAL* 3.1 11.4 + - + +
104D GLN 4.6 0.4 - - - -
105D HIS* 2.9 40.5 + - - -
108D HIS* 3.5 28.6 - + + +
109D SER* 3.4 20.2 - - - -
112D TRP* 3.0 23.8 + - - +
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Residues in contact with SER 64 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35D LEU* 3.7 26.3 - - - +
59D TYR 3.1 9.5 + - - -
60D SER 3.1 30.1 + - - -
61D LYS 4.0 0.7 - - - -
62D HIS 3.3 0.6 - - - -
63D HIS* 1.3 76.3 - - - +
65D ALA* 1.3 55.0 + - - +
67D VAL* 3.4 2.9 + - - +
68D ASP* 3.0 44.9 + - - +
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Residues in contact with ALA 65 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61D LYS 3.1 19.6 + - - +
62D HIS* 3.7 6.7 - - - +
63D HIS 3.2 0.4 - - - -
64D SER* 1.3 76.7 - - - +
66D TYR* 1.3 59.2 + - + +
68D ASP* 3.4 6.8 + - - +
69D LYS* 2.9 32.1 + - - +
101D GLN* 4.6 0.9 - - - -
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Residues in contact with TYR 66 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152C PHE* 4.0 16.4 - + - -
62D HIS* 3.1 32.4 + - + -
63D HIS* 3.0 12.3 + + - +
65D ALA* 1.3 78.5 - - + +
67D VAL* 1.3 58.8 + - - +
70D LEU* 2.9 32.5 + - - +
101D GLN* 3.3 40.0 - - - +
104D GLN* 3.0 44.7 + - + -
105D HIS* 4.4 7.9 - - - +
108D HIS* 3.5 25.8 - + - -
193D TRP* 3.7 18.9 - - - -
195D HIS* 4.3 5.8 - + - -
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Residues in contact with VAL 67 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33D ALA* 3.6 33.8 - - - +
34D GLU* 3.9 6.5 - - - -
35D LEU* 3.9 19.3 - - + +
63D HIS* 3.1 18.1 + - + +
64D SER* 3.7 8.7 - - - +
66D TYR* 1.3 77.2 - - - +
68D ASP* 1.3 68.4 + - - +
70D LEU* 3.3 2.2 + - - +
71D ASN* 3.1 32.6 + - - +
105D HIS* 3.5 36.6 - - + +
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Residues in contact with ASP 68 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64D SER* 3.0 30.5 + - - +
65D ALA* 3.8 6.3 - - - +
67D VAL* 1.3 84.4 - - - +
69D LYS* 1.3 62.7 + - - +
71D ASN* 3.3 16.8 + - - +
72D THR* 3.5 16.0 + - - +
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Residues in contact with LYS 69 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65D ALA 2.9 13.6 + - - +
68D ASP* 1.3 74.2 - - - +
70D LEU* 1.3 66.3 + - - +
72D THR* 2.6 35.8 + - + +
73D LEU* 3.4 15.4 - - + +
97D VAL* 4.0 21.5 - - - -
101D GLN* 3.3 35.2 - - + +
78F GLU* 5.7 7.7 - - - +
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Residues in contact with LEU 70 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31D TYR* 3.5 13.2 + - + -
33D ALA* 3.8 20.4 - - + -
66D TYR 2.9 19.5 + - - +
67D VAL 3.3 5.3 + - - +
69D LYS* 1.3 75.3 - - - +
71D ASN* 1.3 57.2 + - - +
73D LEU* 2.9 19.4 + - - -
74D GLY 3.0 12.3 + - - -
82D ILE* 3.9 21.1 - - + -
85D ILE* 4.4 9.9 - - + -
98D MET* 4.1 23.8 - - + +
101D GLN* 4.0 11.6 - - + +
102D ALA* 4.0 37.9 - - + +
105D HIS* 4.3 5.8 - - + -
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Residues in contact with ASN 71 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31D TYR* 3.3 24.0 + - - -
32D PRO* 3.7 9.4 - - - +
33D ALA* 2.9 46.0 + - - +
67D VAL* 3.1 27.6 + - - +
68D ASP* 3.7 9.3 + - - +
69D LYS 3.2 0.8 - - - -
70D LEU* 1.3 76.7 - - - +
72D THR* 1.3 57.5 + - - +
73D LEU 3.3 0.4 - - - -
75D LYS 5.5 0.2 + - - -
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Residues in contact with THR 72 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68D ASP 3.5 14.1 + - - +
69D LYS* 2.6 30.5 + - + +
71D ASN* 1.3 76.4 - - - +
73D LEU* 1.3 73.3 + - - +
74D GLY 3.9 0.4 - - - -
75D LYS* 5.5 1.4 - - - +
78F GLU* 6.0 4.0 - - - -
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Residues in contact with LEU 73 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69D LYS* 3.4 21.1 - - + +
70D LEU* 2.9 6.3 + - - +
72D THR* 1.3 99.7 - - - +
74D GLY* 1.3 61.9 + - - +
75D LYS* 3.4 6.2 + - - +
77D TYR* 5.4 0.2 - - - -
97D VAL* 3.9 21.1 - - + -
98D MET* 3.4 52.9 - - + +
101D GLN* 4.2 8.3 - - + -
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Residues in contact with GLY 74 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31D TYR* 3.1 29.7 + - - -
70D LEU* 3.0 10.7 + - - -
73D LEU* 1.3 76.2 - - - +
75D LYS* 1.3 67.9 + - - +
77D TYR* 2.9 31.5 + - - +
85D ILE* 5.2 0.4 - - - -
98D MET* 4.1 11.7 - - - -
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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