Contacts of the helix formed by residues 56 - 67 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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52B PRO 5.0 1.6 + - - -
53B ALA 5.6 0.2 - - - -
54B SER 3.4 0.2 - - - -
55B ARG* 1.3 79.6 - - - +
57B VAL* 1.3 53.2 + - - +
58B GLU* 3.4 20.1 + - - +
59B THR* 2.6 34.5 + - - -
60B LEU* 2.8 33.0 + - - +
89B ASN* 3.9 4.7 - - - +
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Residues in contact with VAL 57 (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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55B ARG 3.7 0.6 + - - -
56B SER* 1.3 72.0 - - - +
58B GLU* 1.3 73.7 + - - +
60B LEU* 3.7 8.7 - - - +
61B LYS* 3.1 45.5 + - - +
89B ASN* 3.6 35.0 - - + +
92B THR* 3.9 27.6 - - + -
93B ALA 4.0 8.7 - - - +
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Residues in contact with GLU 58 (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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56B SER* 3.4 19.8 - - - +
57B VAL* 1.3 92.2 + - + +
59B THR* 1.3 62.2 + - - +
61B LYS* 3.7 10.8 + - - +
62B GLU* 3.7 21.3 + - - +
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Residues in contact with THR 59 (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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53B ALA 3.8 21.5 + - - +
54B SER* 3.9 16.6 - - - -
56B SER* 2.6 25.1 + - - -
58B GLU* 1.3 75.5 - - - +
60B LEU* 1.3 65.1 + - - +
62B GLU* 3.0 18.3 + - - +
63B MET* 3.1 23.7 + - + +
370B PRO* 5.1 4.7 - - + -
371B LEU* 4.4 14.1 - - + -
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Residues in contact with LEU 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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50B ILE* 4.0 20.0 - - + -
54B SER 3.4 17.3 - - - +
55B ARG* 3.4 24.5 - - - +
56B SER 2.8 10.9 + - - +
57B VAL* 3.3 1.5 + - - +
59B THR* 1.3 77.2 - - - +
61B LYS* 1.3 59.7 + - - +
63B MET* 3.2 17.6 + - + +
64B ILE* 3.2 18.4 + - + +
68B MET* 4.1 15.7 - - + -
86B THR 4.7 0.2 - - - +
89B ASN* 3.6 9.6 - - + +
90B VAL* 3.5 48.2 - - + +
93B ALA* 3.6 16.4 - - + -
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Residues in contact with LYS 61 (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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57B VAL* 3.1 35.7 + - - +
58B GLU* 3.9 9.6 - - - +
59B THR 3.3 0.2 - - - -
60B LEU* 1.3 75.0 - - - +
62B GLU* 1.3 57.4 + - + +
64B ILE* 3.3 3.8 + - - +
65B LYS* 3.1 34.4 + - + +
92B THR* 5.1 0.7 - - - -
93B ALA* 3.7 13.5 - - + +
96B SER* 3.6 34.4 - - - +
97B PHE* 3.8 17.2 - - + -
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Residues in contact with GLU 62 (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 GLU 3.7 13.4 + - - +
59B THR* 3.0 11.0 + - - +
61B LYS* 1.3 78.2 - - + +
63B MET* 1.3 53.6 + - - +
65B LYS* 3.7 32.2 + - - +
66B SER* 2.7 37.0 + - - -
371B LEU* 3.7 27.4 - - + -
375B ARG* 4.3 9.4 + - - -
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Residues in contact with MET 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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48B CYS* 4.8 0.9 - - - -
50B ILE* 4.6 12.6 - - - -
54B SER* 3.7 27.1 - - - +
59B THR* 3.1 18.1 + - + +
60B LEU* 3.2 14.3 + - + +
62B GLU* 1.3 76.3 - - - +
64B ILE* 1.3 54.4 + - - +
66B SER* 3.3 5.2 + - - -
67B GLY 2.9 9.7 + - - -
68B MET* 2.8 48.7 + - + +
364B THR* 4.1 8.3 - - + -
370B PRO* 3.5 42.4 - - + +
371B LEU* 3.9 10.3 - - + -
374B VAL* 3.5 20.2 - - + +
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Residues in contact with ILE 64 (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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60B LEU* 3.2 16.6 + - + +
61B LYS 3.3 5.1 + - - +
63B MET* 1.3 72.3 - - - +
65B LYS* 1.3 65.6 + - - +
67B GLY* 3.3 11.6 + - - -
68B MET* 4.1 19.6 + - + +
90B VAL* 5.0 0.9 - - + +
93B ALA* 3.8 29.4 - - + +
94B THR* 3.8 23.1 - - - +
97B PHE* 3.9 20.0 - - + -
105B ARG* 3.1 46.8 + - + +
107B VAL* 3.9 20.6 - - + -
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Residues in contact with LYS 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 21.5 + - + +
62B GLU* 3.7 33.6 + - - +
64B ILE* 1.3 77.6 - - - +
66B SER* 1.3 60.3 + - - +
67B GLY* 3.4 0.9 + - - -
97B PHE* 4.0 20.0 - - + -
105B ARG* 3.6 24.6 + - - +
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Residues in contact with SER 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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62B GLU 2.7 25.3 + - - -
63B MET* 3.6 7.0 - - - -
64B ILE 3.3 0.2 - - - -
65B LYS* 1.3 76.0 - - - +
67B GLY* 1.3 57.7 + - - +
371B LEU* 4.2 6.6 + - - +
374B VAL* 3.8 25.3 - - - +
375B ARG* 3.1 44.7 + - - +
378B HIS* 4.1 19.6 + - - +
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Residues in contact with GLY 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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42B ARG* 2.9 29.9 + - - -
46B ILE* 3.7 5.7 - - - +
63B MET 2.9 2.6 + - - -
64B ILE 3.3 7.4 + - - -
65B LYS 3.2 3.9 - - - -
66B SER* 1.3 80.2 - - - +
68B MET* 1.3 66.9 + - - +
69B ASN* 3.3 12.0 - - - +
105B ARG* 5.3 2.7 - - - -
374B VAL* 4.1 6.1 - - - -
378B HIS* 5.3 0.2 - - - -
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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