Contacts of the helix formed by residues 54 - 65 (chain B) in PDB entry 1F4J
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 ASP 54 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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41B VAL* 3.1 12.4 - - - +
42B ILE* 2.6 43.8 + - + +
50B LEU* 4.3 5.6 - - + -
51B LEU 3.0 16.8 + - - +
52B VAL 3.0 3.3 + - - -
53B GLN* 1.3 76.6 - - - +
55B VAL* 1.3 59.9 + - - +
56B VAL 3.1 1.1 + - - +
57B PHE* 3.1 28.3 + - + +
58B THR* 3.4 10.6 + - - -
431C ARG* 2.8 32.4 + - - +
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Residues in contact with VAL 55 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29B THR* 5.5 5.4 - - + -
52B VAL 4.1 7.4 - - - +
53B GLN* 2.7 25.9 + - - +
54B ASP* 1.3 67.3 - - - +
56B VAL* 1.3 70.1 + - + +
58B THR* 3.8 9.8 - - - -
59B ASP* 2.8 33.7 + - + +
337D SER* 3.7 40.8 - - - +
339D MET* 6.3 1.6 - - + -
355D LEU* 4.5 16.4 - - + +
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Residues in contact with VAL 56 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29B THR* 4.2 22.8 - - + +
34B PRO 5.8 0.4 - - - +
35B VAL* 3.8 38.4 - - + -
36B GLY 5.7 0.2 - - - +
37B ASP 4.8 0.7 - - - +
38B LYS* 3.9 20.2 - - + -
54B ASP* 3.0 8.0 + - - +
55B VAL* 1.3 85.7 - - + +
57B PHE* 1.3 64.3 + - - +
59B ASP* 3.4 2.5 + - - +
60B GLU* 3.2 21.2 + - + +
159C ILE* 4.2 5.8 - - + -
431C ARG* 3.7 16.4 - - - +
420D GLU* 4.1 9.2 - - - +
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Residues in contact with PHE 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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52A VAL* 6.2 1.1 - - + -
41B VAL* 4.1 7.4 - - + -
50B LEU* 4.1 24.7 - - + -
54B ASP* 3.1 27.1 + - + +
56B VAL* 1.3 81.9 - - - +
58B THR* 1.3 61.0 + - - +
60B GLU* 3.3 3.1 + - - +
61B MET* 2.7 78.8 + - + +
158C PRO* 3.5 18.4 - - + -
159C ILE* 4.0 30.7 - - + +
353C GLY* 3.8 24.9 - - - -
356C PHE* 4.4 15.7 - + + -
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Residues in contact with THR 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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52A VAL* 6.1 1.2 - - - +
52B VAL* 4.6 7.6 + - - -
54B ASP 3.4 10.7 + - - -
55B VAL* 3.9 10.6 - - - -
56B VAL 3.4 0.4 - - - -
57B PHE* 1.3 86.0 - - - +
59B ASP* 1.3 57.8 + - - +
61B MET* 3.2 4.0 + - - -
62B ALA* 2.7 36.9 + - - +
356C PHE* 3.8 30.2 - - + -
355D LEU 6.1 0.7 - - - +
356D PHE* 4.9 13.5 - - + -
359D PRO* 5.9 4.0 - - + -
363D ARG* 4.5 13.2 - - - +
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Residues in contact with ASP 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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29B THR* 3.6 12.6 - - - -
30B GLY* 2.8 35.1 + - - -
31B ALA 5.5 0.2 - - - -
55B VAL* 2.8 23.2 + - + +
56B VAL* 3.7 5.7 - - - +
58B THR* 1.3 74.2 - - - +
60B GLU* 1.3 62.7 + - - +
62B ALA* 4.1 2.1 - - - +
63B HIS* 3.4 18.0 + - - +
363D ARG* 4.0 18.6 + - - +
371D LEU* 4.7 8.8 - - - +
387D GLN* 2.9 18.5 + - - +
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Residues in contact with GLU 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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38B LYS* 2.9 44.8 + - + +
56B VAL 3.2 13.3 + - - +
57B PHE* 3.8 2.7 - - - +
59B ASP* 1.3 77.2 + - - +
61B MET* 1.3 68.4 + - - +
63B HIS* 3.1 5.0 + - - +
64B PHE* 2.9 20.4 + - - +
159C ILE* 3.5 18.3 - - - +
162C PRO* 4.2 26.7 - - + +
163C SER* 4.8 2.3 + - - -
386D TYR* 4.3 18.9 + - - +
387D GLN* 3.7 25.4 - - + +
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Residues in contact with MET 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 PHE* 2.7 61.5 + - + +
58B THR 3.8 2.0 - - - +
60B GLU* 1.3 75.1 - - - +
62B ALA* 1.3 56.5 + - - +
64B PHE* 3.2 18.2 + - - +
65B ASP* 2.8 54.3 + - - +
158C PRO 3.6 14.4 - - - +
161C PHE* 4.6 0.2 - - + -
162C PRO* 3.9 16.6 - - + -
356C PHE* 4.0 16.4 - - + -
357C ALA* 4.2 5.4 - - + -
600C HEM 3.8 24.9 - - + -
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Residues in contact with ALA 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 THR 2.7 19.2 + - - +
59B ASP 4.1 0.4 - - - +
61B MET* 1.3 73.3 - - - +
63B HIS* 1.3 61.4 + - - +
65B ASP 3.4 6.2 + - - -
66B ARG* 3.0 33.9 + - - +
356C PHE* 4.3 6.0 - - + -
360C ASP* 3.5 13.7 - - - +
363D ARG* 3.1 44.6 - - - +
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Residues in contact with HIS 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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59B ASP 3.4 5.6 + - - +
60B GLU 3.1 7.0 + - - +
62B ALA* 1.3 76.0 - - - +
64B PHE* 1.3 65.8 + - - +
65B ASP 3.0 1.8 - - - -
66B ARG* 2.9 17.2 + - + +
67B GLU* 3.2 11.2 + - - +
368D PRO* 4.3 15.2 - - + +
369D ASN* 2.6 27.5 + - - -
372D HIS* 5.3 1.0 + - - -
387D GLN* 3.4 38.8 - - + +
388D ARG* 3.2 32.6 + - - -
389D ASP 3.2 16.2 - - - -
390D GLY* 4.6 3.3 - - - -
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Residues in contact with PHE 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 GLU* 2.9 12.7 + - + +
61B MET* 3.4 16.4 - - - +
63B HIS* 1.3 75.7 - - - +
65B ASP* 1.3 77.4 + - - +
66B ARG 3.1 1.4 + - - -
67B GLU* 3.2 41.7 + - - +
68B ARG* 5.7 0.2 - - - -
73C VAL* 3.6 43.0 - - + +
74C VAL* 4.2 0.9 - - + -
161C PHE* 3.9 31.4 - + - -
162C PRO* 3.7 31.2 - - + -
165C ILE* 3.8 30.7 - - + -
166C HIS* 4.1 5.4 - + - -
600C HEM 4.3 5.8 - - + -
387D GLN* 5.9 0.4 - - - +
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Residues in contact with ASP 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 MET* 2.8 33.3 + - - +
62B ALA* 3.4 3.8 - - - +
64B PHE* 1.3 91.6 - - - +
66B ARG* 1.3 58.6 + - - +
67B GLU 3.6 0.4 - - - -
68B ARG 5.4 0.3 + - - -
73C VAL* 5.2 3.8 - - - +
356C PHE* 4.2 0.5 - - - -
357C ALA* 3.4 26.7 - - - +
360C ASP* 2.6 31.2 - - - +
361C THR* 2.9 31.9 + - - +
364C HIS* 3.5 12.1 - - - -
600C HEM 3.6 13.1 - - - +
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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