Contacts of the helix formed by residues 51 - 61 (chain A) 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 SER 51 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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45A GLY* 3.7 4.0 - - - -
47A GLN* 3.8 4.7 - - - +
49A VAL 4.1 0.4 + - - -
50A MET* 1.3 74.9 - - - +
52A PRO* 1.3 76.1 - - - +
53A ARG* 3.7 4.8 + - - +
54A GLN 3.2 14.7 + - - -
55A LEU* 3.1 17.8 + - - +
199A LYS* 4.2 3.5 - - - +
200A ASP* 2.5 34.9 + - - -
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Residues in contact with PRO 52 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42A TYR 4.8 2.3 - - - +
43A LYS* 3.3 25.0 - - - +
44A ASP* 4.0 11.2 - - - +
45A GLY* 3.7 12.8 - - - +
47A GLN* 4.2 10.5 - - - +
51A SER* 1.3 90.1 - - - +
53A ARG* 1.3 57.1 + - - +
55A LEU* 3.4 1.2 + - - +
56A GLU* 2.8 32.1 + - - +
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Residues in contact with ARG 53 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51A SER* 3.2 6.0 + - - +
52A PRO* 1.3 78.3 - - - +
54A GLN* 1.3 60.6 + - - +
56A GLU* 3.8 23.5 + - + -
57A LEU* 2.9 40.1 + - + +
199A LYS* 4.1 19.1 - - + +
202B GLU* 2.7 41.5 + - - -
204B ARG* 4.9 2.4 - - - +
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Residues in contact with GLN 54 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50A MET* 4.2 14.1 - - + -
51A SER* 3.2 14.2 + - - +
53A ARG* 1.3 77.9 - - - +
55A LEU* 1.3 57.8 + - - +
57A LEU* 3.9 6.4 - - - +
58A HIS* 3.1 28.6 + - + +
195A HIS 3.0 22.4 + - - -
196A ALA* 3.3 18.4 + - - +
197A TYR* 3.2 29.6 - - - +
199A LYS* 3.2 25.5 + - + +
200A ASP* 3.2 31.4 + - - +
198B TYR* 5.1 2.6 + - - -
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Residues in contact with LEU 55 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38A LEU* 4.2 6.1 - - + -
40A PHE* 3.8 18.8 - - + -
42A TYR* 3.7 27.4 - - - +
45A GLY* 3.8 32.1 - - - +
46A ILE* 4.1 12.8 - - + +
50A MET* 4.7 7.1 - - + +
51A SER 3.1 15.7 + - - +
52A PRO 3.9 1.6 - - - +
54A GLN* 1.3 75.7 - - - +
56A GLU* 1.3 65.4 + - - +
58A HIS* 4.5 1.6 - - - -
59A TYR* 2.9 32.1 + - + +
112A TRP* 3.6 35.7 - - + -
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Residues in contact with GLU 56 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42A TYR* 4.6 13.4 + - + +
43A LYS* 6.4 0.4 - - - -
52A PRO 2.8 23.4 + - - +
53A ARG* 3.8 26.0 + - - +
55A LEU* 1.3 72.9 - - - +
57A LEU* 1.3 62.7 + - + +
59A TYR* 5.1 0.4 - - - -
60A SER* 2.8 49.5 + - - +
61A LYS* 3.6 9.3 + - - +
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Residues in contact with LEU 57 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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53A ARG* 2.9 31.1 + - + +
54A GLN* 3.9 4.9 - - - +
56A GLU* 1.3 79.6 - - + +
58A HIS* 1.3 65.5 + - - +
61A LYS* 3.0 33.9 + - + +
62A HIS* 3.1 12.5 + - + -
199A LYS* 3.7 33.7 - - + -
198B TYR* 3.8 26.0 - - + +
202B GLU* 3.7 27.8 - - + +
203B ASN* 3.7 22.7 - - - +
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Residues in contact with HIS 58 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50A MET* 5.5 4.4 - - - -
54A GLN* 3.1 23.3 + - - +
55A LEU* 3.9 2.7 - - + +
57A LEU* 1.3 78.6 - - - +
59A TYR* 1.3 57.5 + - - +
62A HIS* 3.3 8.9 - - + +
63A HIS* 2.9 27.0 + - - +
108A HIS* 3.1 22.4 + + - -
111A PHE* 4.0 14.9 - + - -
112A TRP* 3.5 20.9 - + + -
191A ASP* 2.7 31.5 + - - -
195A HIS* 3.2 20.6 + + - -
196A ALA* 3.6 30.4 + - + -
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Residues in contact with TYR 59 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35A LEU* 3.8 38.6 + - + +
36A PRO* 2.6 32.3 + - + -
37A THR* 4.6 2.1 - - - -
38A LEU* 3.7 25.3 + - + +
42A TYR* 4.1 34.1 - + + -
55A LEU* 2.9 22.6 + - + +
56A GLU* 5.1 0.2 - - - -
58A HIS* 1.3 77.4 - - - +
60A SER* 1.3 72.6 + - - +
61A LYS 3.3 0.2 - - - -
63A HIS* 3.5 7.2 - - - +
64A SER* 3.1 27.2 + - - -
112A TRP* 3.7 28.9 - + + -
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Residues in contact with SER 60 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35A LEU* 5.0 3.5 - - - +
42A TYR* 3.9 18.2 - - - -
56A GLU* 2.8 33.2 + - - +
59A TYR* 1.3 88.5 - - - +
61A LYS* 1.3 68.6 + - - +
64A SER* 3.2 18.5 + - - -
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Residues in contact with LYS 61 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56A GLU* 4.4 9.0 - - - +
57A LEU* 3.0 31.3 + - + +
60A SER* 1.3 90.0 - - - +
62A HIS* 1.3 66.7 + - - +
63A HIS 3.5 0.2 - - - -
64A SER* 3.6 1.1 + - - -
65A ALA* 3.0 26.7 + - - +
203B ASN* 3.9 40.6 - - + +
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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