Contacts of the helix formed by residues 68 - 84 (chain D) in PDB entry 1F5Q
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 ASN 68 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5D GLU* 4.4 18.8 - - - +
66D ASP* 3.0 3.4 + - + +
67D ASN* 1.3 80.8 - - - +
69D VAL* 1.3 64.7 + - - +
71D PRO* 3.3 11.0 - - - +
72D LEU* 3.4 17.7 + - - +
106D ARG* 3.5 42.6 - - + +
148D LEU* 3.8 4.6 - - + +
150D THR* 2.9 30.1 + - - +
151D ASP* 3.9 8.6 + - - -
171D TYR* 3.8 13.0 + - - -
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Residues in contact with VAL 69 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60D CYS* 4.1 15.0 - - - -
65D GLN* 4.5 6.7 - - + +
66D ASP* 3.0 22.6 + - + +
68D ASN* 1.3 76.2 - - - +
70D PHE* 1.3 61.2 + - - +
72D LEU 3.4 0.3 + - - -
73D ALA* 2.9 27.7 + - - +
99D LEU* 4.1 10.3 - - + +
102D ALA* 3.4 23.4 - - + +
103D GLY* 4.0 8.3 - - - +
106D ARG* 4.0 4.0 - - + -
107D ALA* 3.6 41.5 - - + +
111D ILE* 4.6 7.9 - - + -
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Residues in contact with PHE 70 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53D THR 3.4 20.9 - - - -
56D MET* 4.1 11.2 - - + -
57D PHE* 3.6 28.9 - + + -
60D CYS* 3.9 20.2 - - + -
66D ASP 4.2 2.9 + - - +
67D ASN 5.0 0.2 - - - +
69D VAL* 1.3 79.8 - - - +
71D PRO* 1.3 67.5 - - + +
73D ALA* 3.3 4.4 + - - +
74D VAL* 3.1 46.5 + - + +
175D ARG* 5.8 0.2 - - - +
179D PHE* 3.3 58.8 - + + -
182D LEU* 4.6 5.4 - - + -
183D CYS* 3.8 24.2 - - - -
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Residues in contact with PRO 71 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67D ASN 3.3 17.0 - - - +
68D ASN* 3.3 13.5 - - - +
70D PHE* 1.3 94.9 - - + +
72D LEU* 1.3 61.9 + - - +
74D VAL* 3.1 13.2 + - - +
75D ALA* 3.2 13.9 + - - +
148D LEU* 3.5 27.8 - - + +
150D THR* 4.6 5.8 - - + +
178D ILE* 5.9 0.7 - - + -
179D PHE* 3.3 29.2 - - + -
182D LEU* 4.1 20.7 - - + +
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Residues in contact with LEU 72 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68D ASN 3.4 15.1 + - - +
69D VAL 3.9 2.5 - - - +
71D PRO* 1.3 79.0 - - - +
73D ALA* 1.3 64.1 + - - +
75D ALA* 3.4 2.0 + - - +
76D LEU* 3.1 28.2 + - + +
102D ALA* 3.5 28.7 - - + +
105D VAL* 3.6 27.8 - - + -
106D ARG* 4.0 9.4 - - + +
144D ALA 3.4 23.3 - - - +
145D ASP* 4.1 2.9 - - - +
146D ARG* 3.6 34.5 - - + +
148D LEU* 3.7 15.1 - - + +
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Residues in contact with ALA 73 (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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56D MET* 3.3 25.4 - - + -
69D VAL 2.9 19.0 + - - +
70D PHE 3.4 5.8 - - - +
71D PRO 3.2 0.2 - - - -
72D LEU* 1.3 75.5 - - - +
74D VAL* 1.3 57.4 + - - +
76D LEU* 3.5 1.2 + - - -
77D LEU* 2.9 24.6 + - - +
98D ALA* 3.3 17.4 - - - +
99D LEU* 3.5 24.7 - - + -
102D ALA* 3.7 7.8 - - + +
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Residues in contact with VAL 74 (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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49D ARG* 3.6 15.0 - - - +
53D THR* 4.0 16.6 - - + -
56D MET* 4.7 5.6 - - - -
70D PHE* 3.1 42.5 + - + +
71D PRO* 3.1 11.1 + - + +
73D ALA* 1.3 73.9 - - - +
75D ALA* 1.3 66.2 + - - +
77D LEU* 3.2 7.7 + - + +
78D ASP* 3.0 44.6 + - - +
182D LEU* 4.2 23.6 - - + -
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Residues in contact with ALA 75 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34D ARG* 3.6 40.0 + - - +
71D PRO 3.2 9.7 + - - +
72D LEU 3.4 7.6 + - - +
74D VAL* 1.3 79.9 - - - +
76D LEU* 1.3 59.5 + - - +
78D ASP* 3.9 1.1 + - - -
79D GLU* 3.3 26.2 + - - +
146D ARG* 4.5 13.2 + - + -
148D LEU* 4.5 9.9 - - + -
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Residues in contact with LEU 76 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72D LEU* 3.1 28.9 + - + +
73D ALA 3.9 3.6 - - - +
75D ALA* 1.3 75.7 - - - +
77D LEU* 1.3 66.3 + - - +
79D GLU* 4.0 3.4 - - - +
80D LEU* 3.1 34.6 + - + +
98D ALA* 4.6 11.0 - - + +
101D ILE* 3.9 29.8 - - + -
102D ALA 4.8 0.2 - - - +
140D LEU* 3.8 28.3 - - + -
144D ALA 3.7 21.1 - - - +
146D ARG* 3.8 34.3 - - + +
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Residues in contact with LEU 77 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43D HIS* 5.7 1.1 - - + -
49D ARG* 5.3 4.7 - - + -
52D LEU* 4.2 17.9 - - + -
53D THR* 4.5 14.1 - - + -
56D MET* 4.0 17.7 - - + -
73D ALA 2.9 19.7 + - - +
74D VAL* 3.2 6.9 + - - +
76D LEU* 1.3 77.1 - - - +
78D ASP* 1.3 69.1 + - - +
80D LEU* 3.3 6.1 + - - +
81D PHE* 3.0 57.6 + - + -
94D THR* 3.5 9.9 - - + +
95D ALA* 3.5 33.2 - - + +
98D ALA* 4.1 6.0 - - + +
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Residues in contact with ASP 78 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34D ARG* 4.5 8.8 - - + -
43D HIS* 2.6 32.0 + - - +
44D PHE* 3.6 20.2 - - + -
49D ARG* 2.8 39.5 + - - +
74D VAL* 3.0 22.8 + - - +
75D ALA* 4.1 4.1 - - - +
77D LEU* 1.3 79.2 - - - +
79D GLU* 1.3 60.6 + - - +
81D PHE* 3.1 1.7 + - - +
82D LEU* 2.8 38.9 + - + +
188D ALA 5.5 0.2 - - - +
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Residues in contact with GLU 79 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30D GLU 5.3 0.7 - - - +
33D ALA* 4.1 19.4 - - - +
34D ARG* 3.9 29.8 + - + +
75D ALA 3.3 17.3 + - - +
76D LEU* 3.6 6.0 + - - +
77D LEU 3.4 0.2 - - - -
78D ASP* 1.3 77.9 - - - +
80D LEU* 1.3 51.4 + - - +
82D LEU* 4.6 3.4 - - - -
83D SER* 2.6 49.0 + - - +
139D THR* 5.5 2.4 - - + +
140D LEU* 4.2 17.2 - - + +
146D ARG* 2.8 37.7 + - - -
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Residues in contact with LEU 80 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76D LEU* 3.1 29.2 + - + +
77D LEU* 3.6 5.8 - - - +
78D ASP 3.1 0.6 - - - -
79D GLU* 1.3 76.3 - - - +
81D PHE* 1.3 60.5 + - - +
83D SER* 4.6 1.1 - - - -
84D THR* 2.9 41.1 + - + +
86D ILE* 4.1 2.9 - - + +
94D THR* 4.5 25.4 - - + +
97D VAL* 5.3 4.0 - - + -
98D ALA* 5.2 4.5 - - + -
101D ILE* 5.5 1.6 - - + -
136D SER* 3.9 47.6 - - - +
139D THR* 4.2 14.8 - - + +
140D LEU* 4.2 17.5 - - + -
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Residues in contact with PHE 81 (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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38D VAL* 6.0 0.7 - - - +
43D HIS* 3.4 34.1 - + + +
48D TYR* 3.5 24.7 - + - +
52D LEU* 3.6 22.0 - - + -
77D LEU* 3.0 55.8 + - + -
78D ASP 3.1 1.8 + - - +
80D LEU* 1.3 78.1 - - - +
82D LEU* 1.3 57.1 + - - +
84D THR 3.0 18.7 - - - +
86D ILE* 3.7 25.7 - - + +
91D TYR* 3.7 37.0 - + - -
94D THR* 4.0 6.3 - - + -
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Residues in contact with LEU 82 (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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34D ARG* 3.0 29.2 - - + +
35D MET* 4.8 0.9 - - - -
36D VAL 5.5 0.7 - - - +
37D GLY* 3.4 11.9 - - - -
38D VAL* 3.4 34.5 + - - +
39D ASN 4.4 3.1 - - - +
40D VAL* 3.3 42.0 - - + +
43D HIS* 3.9 21.8 - - + -
44D PHE* 4.1 24.9 - - + -
78D ASP* 2.8 24.6 + - + +
79D GLU 4.3 1.6 - - - +
81D PHE* 1.3 76.4 - - - +
83D SER* 1.3 60.9 + - - +
84D THR 4.7 0.2 - - - -
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Residues in contact with SER 83 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33D ALA 5.7 3.4 - - - -
36D VAL 5.7 2.7 - - - -
37D GLY* 5.5 0.7 - - - -
38D VAL* 5.9 2.9 - - - -
79D GLU* 2.6 32.4 + - - -
82D LEU* 1.3 80.1 - - - +
84D THR* 1.3 62.7 + - - +
139D THR* 3.7 19.2 - - - +
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Residues in contact with THR 84 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38D VAL* 5.9 3.4 - - - +
80D LEU* 2.9 26.1 + - + +
81D PHE 3.0 18.9 - - - +
82D LEU 3.6 0.5 - - - -
83D SER* 1.3 85.7 - - - +
85D ARG* 1.3 70.1 + - - +
86D ILE* 3.6 15.9 + - - +
139D THR* 3.5 33.9 - - + +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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