Contacts of the helix formed by residues 90 - 108 (chain A) in PDB entry 3FZ7
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 TYR 90 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81A ASN* 3.2 19.1 + - + +
82A LYS* 3.8 24.7 - - + -
83A ASN* 3.4 37.0 - - + +
86A ASP* 3.2 20.9 + - + +
87A LYS* 3.5 3.4 - - - +
89A GLU* 1.3 98.8 - - + +
91A PRO* 1.4 65.6 - - - +
92A GLN 3.2 3.3 + - - -
93A SER* 3.3 10.6 + - - +
94A ALA* 3.1 20.3 + - - +
53F ASP* 3.3 16.4 - - + +
54F GLY 3.6 26.7 - - - -
55F ASN 4.8 2.1 - - - -
56F ALA* 3.3 23.6 - - + +
62F THR* 5.7 1.0 - - - +
66F THR* 4.1 5.9 - - - +
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Residues in contact with PRO 91 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87A LYS 3.2 16.1 - - - +
88A GLU* 4.2 7.2 - - - +
89A GLU 3.5 9.2 - - - +
90A TYR* 1.4 88.6 - - - +
92A GLN* 1.3 63.0 + - - +
94A ALA* 3.3 6.2 + - + +
95A ALA* 2.9 26.7 + - - +
52F LEU* 3.9 18.8 - - + +
53F ASP* 3.8 3.4 - - - +
54F GLY 4.6 0.4 - - - +
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Residues in contact with GLN 92 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91A PRO* 1.3 80.2 - - - +
93A SER* 1.3 63.5 + - - +
94A ALA 3.1 1.1 - - - -
95A ALA* 3.2 11.8 + - - +
96A ILE* 3.0 28.2 + - + +
99A ARG* 3.7 15.2 - - - +
436E LEU* 4.3 10.0 - - - +
49F GLU* 3.0 61.0 + - + +
50F LEU* 4.6 2.2 - - - -
52F LEU* 3.3 34.0 - - + +
53F ASP* 3.0 15.3 + - - +
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Residues in contact with SER 93 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82A LYS* 3.5 17.0 - - - +
83A ASN 5.8 0.9 - - - -
84A TRP* 6.0 1.1 - - - -
90A TYR* 3.3 13.2 + - - -
92A GLN* 1.3 76.1 - - - +
94A ALA* 1.3 62.9 + - - +
96A ILE* 3.3 6.4 + - - +
97A ASP* 3.0 24.3 + - - +
321A ALA* 3.9 22.9 - - - +
324A VAL* 5.0 1.6 - - - +
325A ILE* 3.6 11.7 - - - +
50F LEU* 3.9 5.0 - - - +
53F ASP* 2.7 30.2 + - - -
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Residues in contact with ALA 94 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84A TRP 5.8 1.3 - - - -
87A LYS* 3.7 40.4 - - + +
90A TYR 3.1 13.3 + - - +
91A PRO* 3.5 13.7 - - + +
92A GLN 3.1 0.6 - - - -
93A SER* 1.3 77.6 - - - +
95A ALA* 1.3 56.3 + - - +
97A ASP* 3.3 8.7 + - - +
98A LEU* 3.0 35.1 + - + +
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Residues in contact with ALA 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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91A PRO 2.9 15.7 + - - +
92A GLN* 3.6 22.9 - - - +
94A ALA* 1.3 74.8 - - - +
96A ILE* 1.3 64.8 + - - +
98A LEU* 3.2 11.2 + - - +
99A ARG* 2.9 34.5 + - - +
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Residues in contact with ILE 96 (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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92A GLN* 3.0 23.5 + - + +
93A SER* 3.7 5.4 - - - +
94A ALA 3.3 0.2 - - - -
95A ALA* 1.3 75.5 - - - +
97A ASP* 1.3 62.2 + - - +
99A ARG* 3.1 21.2 + - - +
100A CYS* 3.0 20.4 + - - -
324A VAL* 4.4 5.2 - - + -
325A ILE* 4.4 17.3 - - + -
328A TYR* 3.6 34.3 - - + -
46F ILE* 4.3 17.7 - - + -
49F GLU* 3.5 26.2 - - + +
50F LEU* 4.0 25.8 - - + -
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Residues in contact with ASP 97 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84A TRP* 3.4 30.5 + - + +
87A LYS* 4.5 9.7 + - - -
93A SER 3.0 13.9 + - - +
94A ALA* 3.4 11.0 - - - +
96A ILE* 1.3 76.5 - - - +
98A LEU* 1.3 68.2 + - - +
100A CYS* 3.1 11.5 + - - +
101A VAL* 3.1 18.0 + - - +
121A THR* 6.0 0.2 - - - -
122A ASN* 3.2 29.6 + - - +
286A TRP* 4.0 2.8 - - - -
324A VAL* 3.6 22.1 - - + +
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Residues in contact with LEU 98 (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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87A LYS* 6.5 1.1 - - - -
94A ALA* 3.0 22.1 + - + +
95A ALA* 3.2 9.2 + - - +
97A ASP* 1.3 82.5 - - - +
99A ARG* 1.3 63.9 + - - +
101A VAL* 3.2 8.8 + - + +
102A ASN* 3.1 20.4 + - - +
117A GLN* 3.4 47.2 + - + +
310A ILE* 6.3 3.6 - - + -
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Residues in contact with ARG 99 (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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92A GLN* 3.7 14.6 - - - +
95A ALA* 2.9 24.8 + - - +
96A ILE* 3.1 14.2 + - - +
98A LEU* 1.3 76.5 - - - +
100A CYS* 1.3 58.6 + - - +
102A ASN* 3.1 6.6 + - - +
103A MET* 2.9 35.3 + - + +
328A TYR* 3.0 43.2 + - + -
25F THR* 3.4 19.4 + - - -
26F ILE* 4.1 17.4 - - - +
29F SER* 3.7 32.2 - - - +
49F GLU* 2.8 35.7 + - - -
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Residues in contact with CYS 100 (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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96A ILE 3.0 20.7 + - - -
97A ASP 3.1 3.8 + - - +
99A ARG* 1.3 73.8 - - - +
101A VAL* 1.3 65.0 + - - +
103A MET* 4.0 7.6 - - - +
104A VAL* 3.0 29.1 + - - +
286A TRP* 3.5 26.2 - - + -
324A VAL* 4.0 13.7 - - - -
327A GLN* 4.6 0.9 - - - -
328A TYR* 3.7 40.2 - - - -
331A PHE* 4.1 12.1 - - + -
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Residues in contact with VAL 101 (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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97A ASP* 3.1 23.2 + - - +
98A LEU* 3.2 13.0 + - + +
100A CYS* 1.3 76.2 - - - +
102A ASN* 1.3 58.5 + - - +
104A VAL 3.5 0.2 + - - -
105A ALA* 2.8 28.2 + - - +
117A GLN* 4.0 10.8 - - - +
118A ALA* 4.0 19.5 - - + +
120A GLY* 3.9 27.6 - - - +
121A THR* 4.1 10.1 - - - +
122A ASN 4.2 1.8 - - - +
286A TRP* 4.1 19.1 - - + -
288A ILE* 3.7 20.8 - - + +
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Residues in contact with ASN 102 (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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98A LEU 3.1 7.5 + - - +
99A ARG* 3.1 9.6 + - - +
101A VAL* 1.3 78.2 - - - +
103A MET* 1.3 57.1 + - - +
105A ALA* 3.4 2.4 + - - +
106A ASP* 2.9 28.8 + - - +
113A PRO* 5.2 1.0 - - - +
116A GLY 3.5 15.0 + - - +
117A GLN* 3.1 26.5 + - - -
118A ALA* 2.7 34.7 + - - +
29F SER* 3.8 13.7 + - - +
30F LYS* 3.9 25.2 - - - +
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Residues in contact with MET 103 (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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99A ARG* 2.9 24.1 + - + +
100A CYS* 4.0 4.7 - - - +
102A ASN* 1.3 73.7 - - - +
104A VAL* 1.3 60.9 + - - +
106A ASP* 3.4 2.8 + - - +
107A LEU* 2.8 28.9 + - - +
328A TYR* 4.0 29.6 - - + +
331A PHE* 4.1 19.7 - - + -
332A LEU* 5.9 1.6 - - + -
25F THR 5.3 0.7 - - - +
28F GLU 4.1 2.9 - - - +
29F SER* 3.9 26.9 - - - +
31F ARG 3.4 23.6 - - - +
32F PHE* 3.6 26.9 - - + +
33F PRO* 3.9 25.8 - - + -
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Residues in contact with VAL 104 (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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100A CYS 3.0 21.1 + - - +
101A VAL* 4.0 2.9 - - - +
103A MET* 1.3 71.3 - - - +
105A ALA* 1.3 67.8 + - - +
107A LEU* 3.1 9.0 + - + +
108A TRP* 3.0 64.6 + - + -
249A PHE* 4.0 15.5 - - + -
286A TRP* 4.2 20.4 - - + -
288A ILE* 3.8 9.2 - - + -
331A PHE* 3.9 25.8 - - + -
32F PHE* 5.2 0.4 - - + -
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Residues in contact with ALA 105 (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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101A VAL 2.8 19.7 + - - +
102A ASN 3.4 4.7 - - - +
104A VAL* 1.3 74.9 - - - +
106A ASP* 1.3 61.9 + - - +
108A TRP* 3.0 10.7 + - - +
109A HIS 3.2 0.2 + - - -
110A ALA* 3.0 38.6 + - + +
118A ALA* 3.5 24.9 - - + -
288A ILE* 3.9 18.9 - - + +
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Residues in contact with ASP 106 (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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102A ASN 2.9 16.4 + - - +
103A MET 3.6 4.5 - - - +
105A ALA* 1.3 73.5 - - - +
107A LEU* 1.3 67.5 + - - +
109A HIS* 2.8 21.2 + - - +
110A ALA 4.8 4.3 - - - +
336A ARG* 3.5 17.5 + - - -
30F LYS 3.8 11.4 - - - +
31F ARG* 3.4 16.6 - - - +
32F PHE 3.0 22.5 + - - +
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Residues in contact with LEU 107 (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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103A MET 2.8 17.0 + - - +
104A VAL* 3.3 11.9 - - - +
106A ASP* 1.3 74.7 + - - +
108A TRP* 1.3 63.0 + - + +
109A HIS* 3.6 14.7 + - - -
248A GLY 3.9 20.0 - - - +
249A PHE* 4.1 18.4 - - + -
252A PRO* 3.7 21.1 - - + +
253A PHE* 3.7 37.9 - - + -
261A ASP* 4.3 1.2 - - - +
336A ARG* 3.7 30.9 + - - +
32F PHE* 3.8 20.6 - - + +
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Residues in contact with TRP 108 (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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104A VAL* 3.0 38.1 + - + +
105A ALA 3.0 4.7 + - - +
106A ASP 3.0 1.2 - - - -
107A LEU* 1.3 90.0 - - + +
109A HIS* 1.3 69.7 + - - +
110A ALA 3.3 1.6 - - - -
248A GLY* 3.0 27.5 + - - -
249A PHE* 4.5 4.7 - + - -
252A PRO* 4.2 1.6 - - + -
260A TRP* 3.4 28.0 - + - -
261A ASP* 3.4 10.1 - - + -
262A PHE* 3.2 30.8 + + + -
270A ILE* 3.4 44.9 - - + -
272A ALA* 3.5 38.4 - - + -
286A TRP* 4.3 5.6 - - + -
288A ILE* 3.5 24.2 - - + -
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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