Contacts of the helix formed by residues 56 - 67 (chain F) in PDB entry 3SRF
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 56 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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52F PRO 5.1 1.2 + - - -
53F ALA 5.5 0.2 - - - -
54F SER 3.3 1.0 - - - -
55F ARG* 1.3 78.8 - - - +
57F VAL* 1.3 53.0 + - - +
58F GLU* 3.6 19.3 + - - +
59F THR* 2.6 34.5 + - - -
60F LEU* 2.7 36.3 + - - +
89F ASN* 4.4 3.1 - - - +
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Residues in contact with VAL 57 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55F ARG 3.7 1.0 + - - -
56F SER* 1.3 70.4 - - - +
58F GLU* 1.3 64.8 + - - +
60F LEU* 2.9 9.7 + - - +
61F LYS* 2.8 58.9 + - - +
89F ASN* 3.6 35.0 - - - +
92F THR* 4.4 14.6 - - + -
93F ALA* 4.0 17.5 - - + +
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Residues in contact with GLU 58 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56F SER* 3.2 19.1 + - - +
57F VAL* 1.3 88.4 + - + +
59F THR* 1.3 61.3 + - - +
61F LYS* 3.6 14.3 + - - +
62F GLU* 3.2 23.1 + - - +
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Residues in contact with THR 59 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53F ALA 3.6 24.1 + - - +
54F SER* 3.8 17.3 - - - +
56F SER* 2.6 26.6 + - - -
58F GLU* 1.3 76.0 - - - +
60F LEU* 1.3 62.1 + - - +
62F GLU* 3.3 9.9 + - - +
63F MET* 3.2 23.1 + - - +
370F PRO* 5.0 5.4 - - + -
371F LEU* 4.2 17.7 - - + -
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Residues in contact with LEU 60 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50F ILE* 3.9 24.2 - - + -
54F SER 3.2 22.2 - - - +
55F ARG* 3.4 23.6 - - - +
56F SER 2.7 15.2 + - - +
57F VAL 3.4 4.5 - - - +
59F THR* 1.3 70.9 - - - +
61F LYS* 1.3 63.4 + - - +
63F MET* 3.6 8.3 + - - +
64F ILE* 3.3 27.8 + - + +
68F MET* 4.5 10.2 - - + +
86F THR 4.7 0.2 - - - +
89F ASN* 3.6 31.9 - - + +
90F VAL* 3.8 24.0 - - + +
93F ALA* 3.7 12.1 - - + -
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Residues in contact with LYS 61 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57F VAL* 2.8 42.1 + - - +
58F GLU* 3.8 9.9 - - - +
59F THR 3.3 0.4 - - - -
60F LEU* 1.3 73.3 - - - +
62F GLU* 1.3 68.1 + - - +
64F ILE* 3.5 4.7 + - - +
65F LYS* 3.3 28.1 + - + +
92F THR* 5.0 1.8 - - - -
93F ALA* 3.8 20.0 - - + +
96F SER* 3.7 29.8 - - - +
97F PHE* 3.8 14.1 - - + -
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Residues in contact with GLU 62 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58F GLU 3.2 20.8 - - - +
59F THR* 3.3 9.4 + - - +
61F LYS* 1.3 79.2 - - - +
63F MET* 1.3 53.4 + - - +
65F LYS* 3.3 31.8 + - - +
66F SER* 2.8 38.0 + - - -
371F LEU* 3.7 29.3 - - + +
375F ARG* 5.1 5.4 + - - +
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Residues in contact with MET 63 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48F CYS* 3.5 39.3 - - + -
50F ILE* 4.3 7.9 - - + -
54F SER* 3.7 27.4 - - - +
59F THR* 3.2 13.9 + - - +
60F LEU* 3.9 8.3 - - - +
61F LYS 3.4 0.2 - - - -
62F GLU* 1.3 73.7 - - - +
64F ILE* 1.3 60.8 + - - +
66F SER* 3.2 8.2 + - - -
67F GLY 2.8 11.4 + - - -
68F MET* 2.8 39.2 + - + +
364F THR* 3.8 15.9 - - + -
370F PRO* 4.7 4.0 - - + -
371F LEU* 3.6 20.0 - - + -
374F VAL* 3.6 16.9 - - + +
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Residues in contact with ILE 64 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60F LEU* 3.3 15.4 + - + +
61F LYS 3.6 7.0 - - - +
62F GLU 3.3 0.4 - - - -
63F MET* 1.3 76.5 - - - +
65F LYS* 1.3 61.8 + - - +
67F GLY* 3.2 12.1 + - - -
68F MET* 3.8 19.5 + - + +
90F VAL* 4.8 1.3 - - + +
93F ALA* 3.6 34.5 - - + +
94F THR* 3.9 17.3 - - + +
97F PHE* 4.0 18.6 - - + -
105F ARG* 4.2 30.4 - - + +
107F VAL* 3.8 22.9 - - + -
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Residues in contact with LYS 65 (chain F).
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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61F LYS* 3.3 17.1 + - + +
62F GLU* 3.4 34.6 + - - +
64F ILE* 1.3 79.6 - - - +
66F SER* 1.3 61.2 + - - +
67F GLY* 3.1 1.8 + - - -
97F PHE* 4.2 21.8 - - + -
499F ARG* 5.9 0.9 + - - -
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Residues in contact with SER 66 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62F GLU 2.8 26.2 + - - -
63F MET* 3.2 11.3 + - - -
65F LYS* 1.3 71.7 - - - +
67F GLY* 1.3 58.2 + - - +
371F LEU* 4.2 6.2 + - - +
374F VAL* 3.8 28.8 - - - +
375F ARG* 3.5 41.5 + - - +
378F HIS* 4.1 14.7 + - - +
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Residues in contact with GLY 67 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42F ARG* 2.5 33.5 + - - -
46F ILE* 3.7 7.5 - - - +
63F MET 2.8 5.7 + - - -
64F ILE 3.2 7.6 + - - -
65F LYS 3.1 4.7 - - - -
66F SER* 1.3 81.0 - - - +
68F MET* 1.3 63.2 + - - -
69F ASN* 3.3 5.7 - - - +
374F VAL* 3.9 4.0 - - - -
378F HIS* 5.3 1.8 - - - -
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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