Contacts of the helix formed by residues 68 - 84 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6B PHE* 4.1 23.6 - - - +
66B ASP* 2.3 29.4 + - - +
67B ASN* 1.3 72.3 - - - +
69B VAL* 1.3 62.5 + - - +
71B PRO* 3.3 7.5 - - - +
72B LEU* 3.3 23.0 + - - +
106B ARG* 3.1 39.7 - - + +
148B LEU* 3.7 4.8 - - + +
150B THR* 2.9 25.3 + - - +
151B ASP* 3.5 8.9 + - - -
171B TYR* 3.4 18.5 + - - -
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Residues in contact with VAL 69 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60B CYS* 4.1 13.9 - - - -
65B GLN* 4.2 6.1 - - + +
66B ASP* 3.1 34.4 + - + +
68B ASN* 1.3 75.5 - - - +
70B PHE* 1.3 59.0 - - - +
72B LEU 3.3 1.7 + - - -
73B ALA* 2.8 28.1 + - - +
99B LEU* 4.3 5.6 - - + +
102B ALA* 3.4 19.3 - - + +
103B GLY* 4.1 2.0 - - - +
106B ARG* 4.1 6.5 - - + -
107B ALA* 3.9 28.3 - - + +
111B ILE* 3.8 23.3 - - + -
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Residues in contact with PHE 70 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53B THR 3.4 23.1 - - - -
56B MET* 4.3 7.9 - - + -
57B PHE* 3.6 30.1 - + + -
60B CYS* 3.7 22.6 - - + -
66B ASP 4.5 1.6 + - - +
67B ASN* 5.7 0.7 - - - -
69B VAL* 1.3 79.5 - - - +
71B PRO* 1.3 69.6 - - + +
73B ALA* 3.3 5.3 + - + +
74B VAL* 3.0 49.6 + - + +
179B PHE* 3.6 54.3 - + + -
182B LEU* 4.3 10.1 - - + -
183B CYS* 3.7 24.9 - - - -
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Residues in contact with PRO 71 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67B ASN 3.4 12.3 - - - +
68B ASN* 3.3 15.5 - - - +
70B PHE* 1.3 96.5 - - + +
72B LEU* 1.3 60.8 + - - +
74B VAL* 3.3 5.4 + - - +
75B ALA* 3.2 19.9 + - - +
148B LEU* 3.7 28.5 - - + +
150B THR* 4.3 8.5 - - + -
179B PHE* 3.3 30.3 - - + -
182B LEU* 3.9 23.3 - - + +
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Residues in contact with LEU 72 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68B ASN 3.3 12.9 + - - +
69B VAL 3.3 3.9 + - - +
70B PHE 3.3 0.2 - - - -
71B PRO* 1.3 72.7 - - - +
73B ALA* 1.3 67.9 + - - +
74B VAL 3.0 1.8 - - - -
75B ALA* 3.0 3.2 + - - +
76B LEU* 2.9 35.6 + - + +
102B ALA* 3.7 18.4 - - + +
105B VAL* 3.7 31.6 - - + -
106B ARG* 4.0 4.5 - - + -
144B ALA 3.4 22.9 - - - +
145B ASP* 3.8 10.1 - - - +
146B ARG* 3.5 37.5 - - + +
148B LEU* 3.7 14.9 - - + +
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Residues in contact with ALA 73 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56B MET* 3.3 26.4 - - + +
69B VAL 2.8 18.2 + - - +
70B PHE* 3.5 5.8 - - - +
72B LEU* 1.3 76.8 - - - +
74B VAL* 1.3 56.8 + - - +
76B LEU* 3.6 1.1 + - - -
77B LEU* 3.0 28.6 + - - +
98B ALA* 3.4 27.0 - - - +
99B LEU* 3.6 15.5 - - + -
102B ALA* 3.6 3.5 - - + +
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Residues in contact with VAL 74 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49B ARG* 3.6 26.5 - - - +
53B THR* 4.4 15.3 - - + -
56B MET* 4.8 6.5 - - - -
70B PHE* 3.0 52.3 + - + +
71B PRO 3.6 5.4 - - - +
72B LEU 3.0 0.2 - - - -
73B ALA* 1.3 76.9 - - - +
75B ALA* 1.3 64.9 + - - +
76B LEU 3.1 0.2 - - - -
77B LEU* 3.3 6.0 + - + +
78B ASP* 3.1 26.5 + - - +
182B LEU* 4.1 25.8 - - + +
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Residues in contact with ALA 75 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34B ARG* 3.5 38.8 + - - +
71B PRO 3.2 11.1 + - - +
72B LEU 3.0 8.8 + - - +
74B VAL* 1.3 77.3 - - - +
76B LEU* 1.3 61.2 + - - +
78B ASP* 3.7 4.9 + - - +
79B GLU* 3.4 18.9 + - - +
146B ARG* 4.2 15.6 + - + -
148B LEU* 4.4 10.1 - - + -
182B LEU* 5.8 1.5 - - + +
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Residues in contact with LEU 76 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72B LEU* 2.9 30.9 + - + +
73B ALA 3.9 4.0 - - - +
75B ALA* 1.3 76.1 - - - +
77B LEU* 1.3 63.6 + - - +
78B ASP 3.3 0.4 - - - -
79B GLU* 4.0 2.8 - - - +
80B LEU* 3.1 32.7 + - + +
98B ALA* 4.4 14.8 - - + +
101B ILE* 4.0 30.1 - - + -
102B ALA 4.5 0.7 - - - +
140B LEU* 3.9 21.5 - - + +
144B ALA* 3.6 27.6 - - + +
146B ARG* 3.8 31.6 - - + +
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Residues in contact with LEU 77 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43B HIS* 6.0 1.6 - - + +
49B ARG* 5.9 3.6 - - + -
52B LEU* 4.1 23.3 - - + -
53B THR* 4.9 10.3 - - + -
56B MET* 3.8 21.8 - - - -
73B ALA 3.0 18.6 + - - +
74B VAL* 3.3 6.0 + - + +
76B LEU* 1.3 76.9 - - - +
78B ASP* 1.3 60.5 + - - +
80B LEU* 3.3 3.6 + - - +
81B PHE* 3.0 49.9 + - + -
94B THR* 3.4 34.3 - - + +
95B ALA* 3.5 20.4 - - + -
98B ALA* 3.9 5.8 - - + -
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Residues in contact with ASP 78 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34B ARG* 4.1 14.6 - - + -
43B HIS* 3.1 16.4 + - - -
44B PHE* 3.6 20.5 - - + -
49B ARG* 3.0 41.3 + - - +
74B VAL* 3.1 19.0 + - - +
75B ALA* 3.8 7.1 - - - +
76B LEU 3.3 0.2 - - - -
77B LEU* 1.3 79.3 - - - +
79B GLU* 1.3 59.8 + - - +
81B PHE* 3.3 0.9 + - - -
82B LEU* 2.9 36.6 + - - +
182B LEU* 6.0 0.3 - - - +
188B ALA 5.1 2.3 - - - +
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Residues in contact with GLU 79 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30B GLU 5.0 1.9 - - - +
33B ALA* 4.6 11.1 - - - +
34B ARG* 4.0 33.7 + - + +
75B ALA 3.4 13.5 + - - +
76B LEU* 4.2 3.8 - - - +
77B LEU 3.4 0.4 - - - -
78B ASP* 1.3 78.3 - - - +
80B LEU* 1.3 55.2 + - - +
82B LEU* 4.5 3.1 - - + +
83B SER* 2.7 53.6 + - - +
139B THR* 4.9 3.9 - - - +
140B LEU* 3.7 22.5 - - + +
146B ARG* 3.0 32.9 + - - -
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Residues in contact with LEU 80 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76B LEU* 3.1 21.2 + - + +
77B LEU* 3.6 5.6 - - - +
78B ASP 3.2 0.4 - - - -
79B GLU* 1.3 79.9 - - - +
81B PHE* 1.3 60.4 + - - +
83B SER* 4.8 1.6 - - - -
84B THR* 2.6 33.3 + - - +
86B ILE* 3.7 5.8 - - + +
94B THR* 4.4 23.6 - - + +
97B VAL* 5.1 2.5 - - + -
98B ALA* 4.9 11.7 - - + -
101B ILE* 5.5 1.3 - - + -
136B SER* 3.9 47.8 - - - +
139B THR* 3.9 20.0 - - + +
140B LEU* 4.3 15.5 - - + -
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Residues in contact with PHE 81 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38B VAL* 5.1 2.1 - - - +
43B HIS* 3.3 32.8 - + + +
48B TYR* 3.6 23.1 - + - -
52B LEU* 3.6 22.9 - - + -
77B LEU* 3.0 55.4 + - + +
78B ASP 3.3 2.4 + - - +
80B LEU* 1.3 77.7 - - - +
82B LEU* 1.3 60.1 + - - +
84B THR 3.2 15.4 - - - +
86B ILE* 3.8 16.8 - - + +
91B TYR* 3.7 40.6 - + - -
94B THR* 3.6 10.1 - - + -
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Residues in contact with LEU 82 (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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34B ARG* 3.0 28.3 - - + +
35B MET* 3.7 16.4 - - + -
37B GLY* 3.6 14.4 - - - -
38B VAL* 3.3 50.2 + - - +
40B VAL* 3.7 24.9 - - + +
43B HIS* 3.9 22.4 - - + -
44B PHE* 3.8 14.1 - - + -
78B ASP 2.9 22.9 + - - +
79B GLU* 4.2 2.0 - - - +
81B PHE* 1.3 79.7 - - - +
83B SER* 1.3 60.0 + - - +
84B THR 3.5 0.7 - - - -
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Residues in contact with SER 83 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33B ALA 4.7 6.8 + - - -
38B VAL* 5.9 1.8 - - - -
79B GLU* 2.7 40.5 + - - +
82B LEU* 1.3 75.9 + - - +
84B THR* 1.3 67.1 + - - +
139B THR* 4.1 18.9 - - - +
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Residues in contact with THR 84 (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 VAL* 6.1 0.2 - - - +
80B LEU* 2.6 25.9 + - + +
81B PHE 3.2 18.4 - - - +
82B LEU 3.5 1.1 - - - -
83B SER* 1.3 87.9 - - - +
85B ARG* 1.3 67.3 + - - +
86B ILE* 3.8 11.4 + - - +
139B THR* 3.8 30.1 - - + +
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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
------------------------------------------------------------
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