Contacts of the helix formed by residues 80 - 95 (chain A) in PDB entry 1FPQ
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 80 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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78A HIS* 3.2 14.6 - - + -
79A SER* 1.3 81.1 + - - +
81A LEU* 1.3 63.4 + - - +
82A PRO* 3.5 2.7 - - - -
83A ASN* 3.3 27.3 + - - +
84A ARG* 2.9 50.0 + - - +
87A ARG* 5.5 2.4 + - - -
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Residues in contact with LEU 81 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69A ALA* 3.6 35.4 - - + +
72A LEU* 4.1 19.1 - - + -
76A THR* 3.7 18.2 - - - +
77A GLN* 3.8 14.8 - - + -
78A HIS* 3.0 39.1 + - + +
80A ASP* 1.3 74.1 - - - +
82A PRO* 1.3 76.0 - - + +
84A ARG* 3.1 9.2 + - + +
85A LEU* 3.0 35.2 + - + +
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Residues in contact with PRO 82 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65A PRO* 3.3 22.7 - - + +
66A SER* 4.1 28.9 - - - +
69A ALA* 4.0 15.7 - - + -
78A HIS 4.0 2.7 - - - +
79A SER 3.6 15.3 - - - +
80A ASP 3.6 0.7 - - - -
81A LEU* 1.3 95.1 - - + +
83A ASN* 1.3 55.7 + - - +
85A LEU* 3.4 1.0 + - + +
86A ASP* 3.0 24.4 + - - +
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Residues in contact with ASN 83 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80A ASP* 3.3 29.4 + - - +
81A LEU 3.2 0.6 - - - -
82A PRO* 1.3 79.9 - - - +
84A ARG* 1.3 62.0 + - - +
86A ASP* 3.4 12.2 + - - +
87A ARG* 2.9 47.8 + - - +
336A ARG* 6.2 3.2 - - - +
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Residues in contact with ARG 84 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78A HIS* 3.3 33.7 + - - -
80A ASP* 2.9 37.3 + - - +
81A LEU* 3.1 10.2 + - + +
83A ASN* 1.3 73.9 - - - +
85A LEU* 1.3 67.1 + - + +
87A ARG* 3.3 22.2 + - - +
88A MSE 3.4 18.9 + - + +
330A PHE* 3.7 42.7 - - + -
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Residues in contact with LEU 85 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47A LEU* 4.5 5.6 - - + -
49A LEU* 4.3 17.0 - - + -
65A PRO* 3.9 6.1 - - + +
68A ILE* 4.3 9.6 - - + -
69A ALA* 3.6 43.5 - - + +
72A LEU* 4.1 17.5 - - + -
81A LEU* 3.0 24.6 + - + +
82A PRO* 3.7 4.0 - - + +
84A ARG* 1.3 75.9 - - + +
86A ASP* 1.3 54.9 + - - +
88A MSE 3.0 29.9 + - + +
89A LEU* 2.8 48.6 + - + +
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Residues in contact with ASP 86 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65A PRO* 3.5 17.6 - - + +
82A PRO 3.0 17.3 + - - +
83A ASN* 3.6 13.5 - - - +
84A ARG 3.3 0.2 - - - -
85A LEU* 1.3 78.4 - - - +
87A ARG* 1.3 57.9 + - - +
89A LEU* 4.2 4.4 - - - +
90A ARG* 2.9 30.7 + - - +
112A ARG* 2.5 34.4 + - - +
114A TYR* 2.8 31.7 + - - -
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Residues in contact with ARG 87 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80A ASP* 5.5 2.4 + - - -
83A ASN* 2.9 34.6 - - - +
84A ARG* 3.5 16.9 - - - +
85A LEU 3.2 0.4 - - - -
86A ASP* 1.3 79.2 - - + +
88A MSE 1.3 61.2 + - - +
90A ARG* 3.6 16.6 - - - +
91A LEU 3.7 1.4 + - - -
323A SER* 4.8 1.0 + - - +
326A ASP* 2.9 56.0 + - - +
327A ASN* 3.1 26.1 + - - +
330A PHE* 3.3 34.3 - - + +
334A GLY 5.7 0.8 + - - -
335A GLY 2.8 28.1 + - - -
336A ARG* 3.1 12.9 - - - +
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Residues in contact with MSE 88 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40A VAL* 4.1 19.7 - - + +
43A ALA* 4.9 13.7 - - - -
44A ALA* 5.2 1.6 - - + -
47A LEU* 4.2 15.9 - - + -
49A LEU* 3.8 17.3 - - + -
84A ARG* 3.4 9.8 + - + +
85A LEU* 3.0 45.4 + - + +
87A ARG* 1.3 75.9 - - - +
89A LEU* 1.3 65.7 + - + +
91A LEU* 3.1 7.4 + - - +
92A LEU* 3.0 29.2 + - + +
327A ASN* 3.7 17.5 - - - +
330A PHE* 6.4 2.5 - - + -
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Residues in contact with LEU 89 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49A LEU* 4.2 24.2 - - + -
53A ILE* 4.6 11.0 - - + -
65A PRO* 4.1 11.9 - - + -
68A ILE* 3.7 21.1 - - + -
85A LEU* 2.8 34.7 + - + +
86A ASP 3.8 0.9 - - - +
88A MSE 1.3 72.1 - - - +
90A ARG* 1.3 57.9 + - - +
92A LEU* 3.2 10.3 + - + +
93A ALA* 2.8 31.2 + - - +
98A LEU* 3.7 19.5 - - + +
114A TYR* 3.4 43.2 - - + +
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Residues in contact with ARG 90 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86A ASP* 2.9 17.1 + - - +
87A ARG* 3.6 11.0 - - - +
88A MSE 3.1 0.2 - - - -
89A LEU* 1.3 76.7 - - - +
91A LEU* 1.3 58.5 + - - +
93A ALA* 3.3 2.9 + - - +
94A SER* 2.8 32.6 + - - -
112A ARG* 3.6 23.8 - - - +
114A TYR* 3.5 15.0 + - - +
309A LEU* 3.9 29.8 - - - +
310A PRO* 2.9 25.0 + - - +
311A GLU 2.9 26.9 + - - -
312A GLU 3.9 0.6 - - - -
313A PRO* 3.6 38.8 - - + +
323A SER* 3.6 15.9 + - - +
326A ASP* 5.4 3.1 - - - -
339A THR* 3.9 12.3 - - - +
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Residues in contact with LEU 91 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36A VAL* 4.4 8.7 - - + -
37A TYR* 4.4 14.1 - - + -
40A VAL* 3.7 35.0 - - + -
87A ARG 3.7 1.6 + - - -
88A MSE 3.1 9.5 + - - +
90A ARG* 1.3 78.5 - - - +
92A LEU* 1.3 64.2 + - + +
94A SER* 3.0 13.6 + - - -
95A TYR* 3.1 40.3 + - + -
320A LYS 4.0 8.1 - - - +
323A SER* 3.9 15.6 + - - +
324A THR* 3.7 17.5 - - - +
327A ASN* 3.8 19.7 - - - +
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Residues in contact with LEU 92 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37A TYR* 4.5 13.0 - - + -
40A VAL* 4.4 10.3 - - + -
41A LEU* 4.5 19.1 - - + -
44A ALA* 3.9 25.4 - - + -
49A LEU* 5.3 0.9 - - + -
50A PHE* 3.9 22.7 - - + -
88A MSE 3.0 19.1 + - + +
89A LEU* 3.6 13.7 - - + +
91A LEU* 1.3 80.9 - - + +
93A ALA* 1.3 58.8 + - - +
95A TYR* 3.3 6.2 + - - -
97A VAL* 3.0 44.3 + - + +
98A LEU* 3.7 22.4 - - + -
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Residues in contact with ALA 93 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89A LEU 2.8 17.1 + - - +
90A ARG 3.7 4.3 - - - +
92A LEU* 1.3 72.6 - - - +
94A SER* 1.3 64.9 + - - +
95A TYR 3.0 2.0 - - - -
96A SER* 3.0 14.2 + - - -
98A LEU* 3.5 22.5 - - + +
100A SER* 4.1 14.8 - - - -
114A TYR* 4.0 19.5 - - + -
313A PRO* 4.4 9.4 - - + +
314A ASN* 4.4 3.4 - - - +
315A THR* 4.0 9.2 - - - +
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Residues in contact with SER 94 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90A ARG 2.8 19.2 + - - -
91A LEU* 3.0 12.3 + - - -
93A ALA* 1.3 76.9 - - - +
95A TYR* 1.3 59.2 + - - +
96A SER 3.3 1.1 + - - -
313A PRO* 4.1 2.9 - - - +
314A ASN 3.1 16.1 + - - +
315A THR* 3.6 13.4 - - - -
319A SER* 2.7 28.5 + - - -
320A LYS* 3.3 42.4 - - - -
323A SER* 4.0 1.7 + - - -
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Residues in contact with TYR 95 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30A VAL* 3.9 23.9 + - - +
34A ASN* 6.0 1.9 - - - -
37A TYR* 3.2 64.1 + + + +
91A LEU* 3.1 47.6 + - + +
92A LEU 3.3 4.9 + - - +
93A ALA 3.0 0.8 - - - -
94A SER* 1.3 79.6 - - - +
96A SER* 1.3 68.4 + - - +
97A VAL* 3.2 7.6 + - + +
119A VAL* 5.8 1.0 - - - +
320A LYS* 3.9 33.3 - - + +
324A THR* 4.7 5.8 + - - -
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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