Contacts of the helix formed by residues 54 - 65 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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431A ARG* 2.7 27.2 + - - +
41D VAL* 2.8 10.8 - - + +
42D ILE* 2.6 49.2 + - + +
50D LEU* 4.5 1.8 - - + -
51D LEU 3.1 15.8 + - - +
52D VAL 2.9 4.5 + - - +
53D GLN* 1.3 76.8 - - - +
55D VAL* 1.3 58.1 + - - +
56D VAL 3.2 0.2 - - - -
57D PHE* 2.8 34.6 + - + +
58D THR* 3.5 13.9 + - - -
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Residues in contact with VAL 55 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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431A ARG* 5.2 0.2 - - - +
337B SER* 3.5 43.5 - - - +
338B ASN* 6.1 0.2 - - - +
339B MET* 6.1 0.7 - - + -
355B LEU* 4.4 18.6 - - + +
359B PRO* 6.3 0.7 - - + -
29D THR* 5.6 5.4 - - + -
52D VAL 4.3 6.5 - - - +
53D GLN 2.6 20.9 + - - +
54D ASP* 1.3 70.3 - - - +
56D VAL* 1.3 68.7 + - + +
58D THR* 3.9 6.8 - - - -
59D ASP* 2.9 30.3 + - + +
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Residues in contact with VAL 56 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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159A ILE* 4.4 5.2 - - + -
431A ARG* 3.6 24.0 - - - +
420B GLU* 4.3 7.6 - - - +
29D THR* 4.0 23.6 - - + -
34D PRO 5.6 1.8 - - - +
35D VAL* 3.9 38.8 - - + -
36D GLY 5.9 0.2 - - - +
37D ASP 4.9 0.7 - - - +
38D LYS* 4.1 17.5 - - + -
54D ASP* 3.2 1.0 - - - +
55D VAL* 1.3 81.3 - - + +
57D PHE* 1.3 62.9 + - - +
59D ASP* 3.6 2.3 - - - +
60D GLU* 3.2 21.4 + - + +
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Residues in contact with PHE 57 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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158A PRO* 3.6 20.0 - - + -
159A ILE* 3.9 31.6 - - + +
353A GLY* 3.7 27.6 - - - -
356A PHE* 4.5 12.8 - + + -
52C VAL* 6.0 2.9 - - + -
41D VAL* 3.7 12.8 - - + -
50D LEU* 3.9 23.3 - - + -
51D LEU 6.1 0.4 - - - -
54D ASP* 2.8 27.7 + - + +
56D VAL* 1.3 77.6 - - - +
58D THR* 1.3 65.6 + - - +
60D GLU* 3.3 2.0 + - - +
61D MET* 2.8 72.5 + - + +
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Residues in contact with THR 58 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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356A PHE* 3.7 29.1 - - + -
355B LEU 6.1 0.9 - - - +
356B PHE* 5.1 11.2 - - + -
359B PRO* 6.2 0.9 - - + -
363B ARG* 4.7 9.9 - - - +
52C VAL* 5.8 3.3 - - - +
52D VAL* 4.4 8.8 + - - -
54D ASP 3.5 11.1 + - - -
55D VAL* 3.4 10.2 + - - -
56D VAL 3.4 0.2 - - - -
57D PHE* 1.3 87.1 - - - +
59D ASP* 1.3 55.6 + - - +
61D MET* 4.3 3.8 - - - -
62D ALA* 2.6 42.3 + - + +
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Residues in contact with ASP 59 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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363B ARG* 4.1 17.4 + - - +
371B LEU* 4.7 8.1 - - - +
387B GLN* 2.9 19.8 + - - +
29D THR* 3.4 13.8 - - - +
30D GLY* 2.9 33.7 + - - -
31D ALA 5.0 0.7 + - - -
55D VAL* 2.9 24.4 + - + +
56D VAL* 3.6 5.9 - - - +
58D THR* 1.3 79.3 - - - +
60D GLU* 1.3 61.7 + - - +
62D ALA* 4.1 1.7 - - - +
63D HIS* 3.4 20.1 + - - +
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Residues in contact with GLU 60 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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159A ILE* 3.3 24.8 - - - +
162A PRO* 4.5 20.8 - - + +
163A SER* 4.5 4.5 + - - -
386B TYR* 4.5 15.8 + - - +
387B GLN* 3.7 28.9 - - + +
38D LYS* 3.1 46.1 + - + +
56D VAL* 3.2 13.4 + - + +
57D PHE* 3.8 2.3 - - - +
59D ASP* 1.3 80.2 - - - +
61D MET* 1.3 61.9 + - - +
63D HIS* 3.3 4.5 + - - +
64D PHE* 3.1 21.3 + - - +
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Residues in contact with MET 61 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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158A PRO 3.4 25.8 - - - +
161A PHE* 4.4 0.2 - - + -
162A PRO* 3.9 17.0 - - + -
356A PHE* 4.0 13.5 - - + -
357A ALA* 4.0 16.6 - - + -
600A HEM 3.6 29.6 - - + -
57D PHE* 2.8 45.9 + - + +
58D THR 3.8 1.8 - - - +
60D GLU* 1.3 73.5 - - - +
62D ALA* 1.3 59.5 + - - +
64D PHE* 3.4 17.1 + - - +
65D ASP* 2.9 45.0 + - - +
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Residues in contact with ALA 62 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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356A PHE* 4.1 8.0 - - + -
360A ASP* 3.5 14.6 - - - +
363B ARG* 3.3 40.4 - - - +
58D THR 2.6 22.3 + - - +
59D ASP 4.1 0.2 - - - +
61D MET* 1.3 73.9 - - - +
63D HIS* 1.3 60.7 + - - +
65D ASP* 3.4 2.6 - - - +
66D ARG* 2.9 37.3 + - - +
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Residues in contact with HIS 63 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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363B ARG* 5.5 0.2 - - - +
368B PRO* 4.2 16.5 - - + +
369B ASN* 2.9 26.0 + - - -
372B HIS* 5.4 1.4 + - - -
387B GLN* 3.5 32.5 - - + +
388B ARG* 3.1 40.9 + - - -
389B ASP 3.3 14.5 + - - -
390B GLY* 4.6 2.6 - - - -
59D ASP 3.4 6.2 + - - +
60D GLU 3.3 7.3 + - - +
61D MET 3.1 0.8 - - - -
62D ALA* 1.3 76.3 - - - +
64D PHE* 1.3 66.6 + - - +
65D ASP 3.0 1.1 - - - -
66D ARG* 2.7 17.5 + - + +
67D GLU* 3.2 10.4 + - + +
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Residues in contact with PHE 64 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73A VAL* 3.5 45.5 - - + +
74A VAL* 4.6 1.3 - - + -
161A PHE* 3.8 29.8 - + - -
162A PRO* 3.8 28.7 - - + -
165A ILE* 3.6 35.9 - - + -
166A HIS* 4.2 3.4 - + - -
600A HEM 4.5 3.6 - - + -
60D GLU 3.1 11.7 + - - +
61D MET* 3.6 16.2 - - - +
63D HIS* 1.3 77.2 + - - +
65D ASP* 1.3 75.6 + - - +
66D ARG 3.0 1.2 + - - -
67D GLU* 3.1 46.0 + - - +
68D ARG* 5.5 0.4 - - - -
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Residues in contact with ASP 65 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73A VAL* 5.1 3.5 - - - +
356A PHE* 4.0 1.7 - - - -
357A ALA* 3.2 29.1 - - - +
360A ASP* 2.6 30.0 - - - +
361A THR* 2.8 30.9 + - - -
364A HIS* 3.5 11.3 - - - -
600A HEM 3.6 19.1 - - - +
61D MET* 2.9 30.1 + - - +
62D ALA 3.4 4.5 - - - +
64D PHE* 1.3 86.0 - - - +
66D ARG* 1.3 59.0 + - - +
67D GLU 3.6 0.4 - - - -
68D ARG 5.5 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