Contacts of the helix formed by residues 56 - 65 (chain B) in PDB entry 4FDI
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 THR 56 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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45B ASP 3.9 13.7 - - - +
46B LEU* 3.6 10.6 - - + +
47B GLY* 2.8 27.3 + - - +
54B ARG 3.6 1.6 - - - -
55B GLU* 1.3 83.4 - - + +
57B PRO* 1.3 59.5 - - - +
59B LEU* 3.4 10.7 + - + -
60B ASP* 3.0 33.9 + - - +
258B VAL* 3.6 30.7 - - + -
262B ASP* 3.3 18.8 - - + +
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Residues in contact with PRO 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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54B ARG 4.9 3.1 - - - +
55B GLU* 3.3 11.0 - - - +
56B THR* 1.3 89.4 - - - +
58B ASN* 1.3 64.0 + - - +
60B ASP* 3.5 8.5 + - + +
61B ARG* 3.0 42.4 + - - +
259B ARG* 6.2 2.7 - - - +
262B ASP* 3.2 11.0 - - - +
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Residues in contact with ASN 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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57B PRO* 1.3 81.6 - - - +
59B LEU* 1.3 62.7 + - + +
61B ARG* 3.4 28.2 + - - +
62B MET* 2.9 25.6 + - - +
262B ASP* 2.8 44.1 + - - +
263B ASP* 3.6 17.0 + - - +
265B ILE* 5.4 1.8 - - + -
266B GLY* 3.4 26.6 - - - +
269B LEU* 4.8 5.4 - - - +
270B GLU* 4.6 4.7 - - - +
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Residues in contact with LEU 59 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41B MET* 5.3 3.8 - - + -
46B LEU* 3.9 27.1 - - + -
48B VAL* 5.0 0.9 - - - -
56B THR* 4.0 9.2 - - + +
58B ASN* 1.3 70.7 - - - +
60B ASP* 1.3 60.4 + - - +
62B MET* 3.2 12.8 + - - -
63B ALA* 3.0 23.7 + - - +
258B VAL* 5.9 0.7 - - + +
261B ILE* 5.7 2.0 - - + -
262B ASP* 2.8 31.1 + - + +
265B ILE* 3.9 28.7 - - + -
285B PHE* 3.7 55.0 - - + -
323B LEU* 3.3 13.2 - - + +
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Residues in contact with ASP 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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46B LEU* 4.4 0.9 - - - +
47B GLY* 3.6 9.0 - - - -
48B VAL* 2.9 49.9 + - + +
54B ARG* 4.5 8.3 - - - +
56B THR* 3.0 35.3 + - - +
57B PRO* 3.7 8.2 - - + +
59B LEU* 1.3 74.3 - - - +
61B ARG* 1.3 58.2 + - - +
63B ALA* 3.3 4.3 + - - +
64B ALA* 3.0 27.4 + - - +
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Residues in contact with ARG 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 PRO* 3.0 32.3 + - - +
58B ASN* 3.5 28.7 + - - +
60B ASP* 1.3 74.3 - - - +
62B MET* 1.3 58.8 + - - +
64B ALA* 3.2 7.9 + - + +
65B GLU* 2.9 57.4 + - + +
270B GLU* 4.3 13.9 + - - +
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Residues in contact with MET 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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36B LEU* 4.7 4.9 - - - -
58B ASN 2.9 14.4 + - - +
59B LEU* 3.2 20.1 + - + +
61B ARG* 1.3 75.5 - - - +
63B ALA* 1.3 57.0 + - - +
65B GLU* 3.3 1.7 + - - -
66B GLY* 3.0 24.4 + - - -
265B ILE* 4.8 0.4 - - - -
269B LEU* 4.0 20.1 - - + +
283B VAL* 3.6 30.1 - - + +
285B PHE* 3.8 16.6 - - + +
323B LEU* 3.7 44.4 - - + +
324B ALA 4.7 1.0 - - - +
325B TRP* 3.5 38.9 - - + +
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Residues in contact with ALA 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 VAL* 4.1 24.7 - - + -
59B LEU 3.0 12.9 + - - +
60B ASP 3.4 9.0 - - - +
61B ARG 3.2 0.2 - - - -
62B MET* 1.3 76.4 - - - +
64B ALA* 1.3 61.2 + - - +
66B GLY 3.1 24.8 + - - +
67B LEU* 4.8 2.1 - - - +
68B LEU* 4.2 7.0 + - + +
323B LEU* 3.8 27.5 - - + +
333B GLY* 3.8 4.9 - - - -
334B GLN 5.0 0.9 - - - +
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Residues in contact with ALA 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 ASP 3.0 16.1 + - - +
61B ARG* 3.2 9.8 + - + +
63B ALA* 1.3 76.9 - - - +
65B GLU* 1.3 60.0 + - + +
332B ALA* 3.6 5.4 - - - +
333B GLY* 3.0 24.0 + - - -
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Residues in contact with GLU 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 ARG* 2.9 42.3 + - + +
62B MET* 3.5 1.5 - - - -
63B ALA 3.1 0.2 - - - -
64B ALA* 1.3 78.1 - - + +
66B GLY* 1.3 55.7 + - - +
269B LEU* 5.4 1.9 - - - +
273B GLN* 4.3 11.1 + - - -
325B TRP* 2.9 42.0 + - + +
326B TRP 5.3 1.7 + - - -
327B PRO* 5.5 7.2 - - + +
330B VAL 4.3 5.5 - - - +
332B ALA* 3.5 23.2 + - + +
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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