Contacts of the helix formed by residues 90 - 108 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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81D ASN* 3.2 18.9 + - + +
82D LYS* 3.7 24.5 - - + -
83D ASN* 3.4 35.4 - - + +
86D ASP* 3.2 22.8 + - + +
87D LYS* 3.7 4.1 - - - +
89D GLU* 1.3 101.5 - - + +
91D PRO* 1.3 57.5 - - - +
93D SER* 3.4 11.5 + - - -
94D ALA* 3.0 26.5 + - - +
53E ASP* 3.0 24.5 - - + +
54E GLY 3.5 22.2 - - - -
55E ASN 4.4 3.0 + - - -
56E ALA* 3.2 23.6 - - + +
66E THR* 4.1 5.7 - - - +
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Residues in contact with PRO 91 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87D LYS 3.3 14.6 - - - +
88D GLU 3.4 10.8 - - - +
89D GLU 3.2 11.2 - - - +
90D TYR* 1.3 90.9 - - - +
92D GLN* 1.3 60.8 + - + +
94D ALA* 3.4 5.8 + - + +
95D ALA* 2.9 27.5 + - - +
52E LEU* 4.0 15.0 - - + +
53E ASP* 3.7 6.3 - - - +
54E GLY 4.4 0.4 - - - +
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Residues in contact with GLN 92 (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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91D PRO* 1.3 80.6 - - - +
93D SER* 1.3 65.7 + - - +
95D ALA* 3.0 13.6 + - - +
96D ILE* 3.0 32.2 + - + +
99D ARG* 3.8 14.8 - - - +
49E GLU* 3.0 63.4 + - + +
50E LEU* 4.2 2.2 - - - +
52E LEU* 3.7 24.5 - - + +
53E ASP* 2.8 19.8 + - - +
436F LEU* 4.5 7.4 - - - +
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Residues in contact with SER 93 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82D LYS* 3.4 18.4 - - - +
83D ASN 5.8 1.1 - - - -
84D TRP* 5.9 1.8 - - - -
90D TYR* 3.8 13.7 - - - -
92D GLN* 1.3 75.6 - - - +
94D ALA* 1.3 63.3 + - - +
96D ILE* 3.1 7.3 + - - +
97D ASP* 2.9 23.5 + - - +
321D ALA* 3.9 21.7 - - - +
324D VAL* 4.8 2.4 - - - +
325D ILE* 3.6 10.0 - - - +
50E LEU* 4.0 4.1 - - - +
53E ASP* 2.7 27.4 + - - -
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Residues in contact with ALA 94 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84D TRP 5.9 0.4 - - - -
87D LYS* 4.0 38.8 - - + +
90D TYR 3.0 14.2 + - - +
91D PRO* 3.5 12.6 - - + +
93D SER* 1.3 76.5 - - - +
95D ALA* 1.3 61.8 + - - +
97D ASP* 3.4 8.7 + - - +
98D LEU* 3.0 32.1 + - + +
310D ILE* 5.8 1.8 - - + -
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Residues in contact with ALA 95 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91D PRO 2.9 17.5 + - - +
92D GLN* 3.0 26.2 + - - +
94D ALA* 1.3 72.6 - - - +
96D ILE* 1.3 63.7 + - - +
98D LEU* 3.1 13.7 + - - +
99D ARG* 3.0 35.7 + - - +
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Residues in contact with ILE 96 (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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92D GLN* 3.0 16.4 + - - +
93D SER* 3.6 6.3 - - - +
95D ALA* 1.3 75.0 - - - +
97D ASP* 1.3 63.7 + - - +
99D ARG* 3.2 18.3 + - - +
100D CYS* 3.0 21.1 + - - -
324D VAL* 4.3 13.0 - - + +
325D ILE* 4.4 9.6 - - + -
328D TYR* 3.5 35.4 - - + -
46E ILE* 4.3 18.2 - - + -
49E GLU* 4.0 25.4 - - + +
50E LEU* 3.8 29.6 - - + -
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Residues in contact with ASP 97 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84D TRP* 3.4 28.3 + - + +
87D LYS* 4.2 9.1 + - - +
93D SER 2.9 16.6 + - - +
94D ALA* 3.6 8.3 - - - +
96D ILE* 1.3 77.3 - - - +
98D LEU* 1.3 69.2 + - - +
100D CYS* 3.2 6.3 + - - +
101D VAL* 3.1 24.6 + - - +
122D ASN* 3.2 28.5 + - - +
286D TRP* 3.9 4.7 - - - -
324D VAL* 3.7 20.8 - - + +
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Residues in contact with LEU 98 (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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87D LYS* 6.5 1.3 - - - -
94D ALA* 3.0 24.7 + - + +
95D ALA* 3.1 11.8 + - - +
97D ASP* 1.3 80.1 - - - +
99D ARG* 1.3 65.1 + - - +
101D VAL* 3.3 6.5 + - + +
102D ASN* 3.1 13.5 + - - +
117D GLN* 2.9 50.8 + - + +
310D ILE* 5.4 18.8 - - + -
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Residues in contact with ARG 99 (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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92D GLN* 3.8 14.3 - - - +
95D ALA* 3.0 21.9 + - - +
96D ILE* 3.2 15.9 + - - +
98D LEU* 1.3 75.3 - - - +
100D CYS* 1.3 64.5 + - - +
102D ASN* 3.1 5.7 + - - +
103D MET* 2.9 32.9 + - + +
328D TYR* 3.1 43.6 + - + -
25E THR* 3.3 33.2 + - - -
26E ILE* 4.1 15.6 - - - +
29E SER* 4.2 27.1 - - - +
49E GLU* 2.7 29.5 + - - -
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Residues in contact with CYS 100 (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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96D ILE 3.0 18.9 + - - -
97D ASP 3.2 6.9 + - - +
99D ARG* 1.3 77.3 - - - +
101D VAL* 1.3 62.1 + - - +
103D MET* 3.1 2.5 + - - +
104D VAL* 2.9 30.9 + - - +
286D TRP* 3.2 31.4 - - + -
324D VAL* 3.9 12.3 - - - -
328D TYR* 3.7 37.7 - - - -
331D PHE* 4.3 15.9 - - + -
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Residues in contact with VAL 101 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97D ASP* 3.1 22.1 + - - +
98D LEU* 3.7 11.2 - - + +
99D ARG 3.2 0.2 - - - -
100D CYS* 1.3 75.1 - - - +
102D ASN* 1.3 66.8 + - - +
104D VAL* 3.3 0.4 + - - -
105D ALA* 2.9 22.3 + - - +
117D GLN* 4.1 5.6 - - - +
118D ALA* 4.1 15.3 - - + +
120D GLY* 3.7 34.8 - - - +
121D THR* 4.2 15.7 - - - -
122D ASN 4.4 1.6 - - - +
286D TRP* 4.0 18.8 - - + -
288D ILE* 3.8 12.6 - - + +
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Residues in contact with ASN 102 (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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98D LEU 3.1 9.2 + - - +
99D ARG* 3.1 7.5 + - - +
101D VAL* 1.3 78.0 - - - +
103D MET* 1.3 55.2 + - - +
105D ALA* 3.4 5.2 + - - +
106D ASP* 2.9 28.4 + - - +
113D PRO* 4.8 2.2 - - - +
116D GLY 3.5 14.6 + - - -
117D GLN* 3.2 27.7 + - - +
118D ALA* 2.9 33.0 + - - +
29E SER 4.2 12.7 + - - +
30E LYS* 3.8 26.7 - - - +
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Residues in contact with MET 103 (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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99D ARG* 2.9 23.2 + - + +
100D CYS 3.1 3.1 + - - +
102D ASN* 1.3 74.3 - - - +
104D VAL* 1.3 62.0 + - - +
106D ASP* 3.2 2.4 + - - +
107D LEU* 2.9 28.4 + - - +
328D TYR* 4.1 28.7 - - + +
331D PHE* 4.0 21.8 - - + -
332D LEU* 5.3 2.5 - - + -
25E THR 5.7 0.7 - - - +
28E GLU 4.4 2.0 - - - +
29E SER* 4.4 24.2 - - - +
31E ARG 3.7 24.5 - - - +
32E PHE* 3.6 28.1 - - + +
33E PRO* 3.8 26.0 - - + -
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Residues in contact with VAL 104 (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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100D CYS 2.9 17.6 + - - +
101D VAL* 3.9 3.1 - - - +
103D MET* 1.3 74.5 - - - +
105D ALA* 1.3 66.1 + - - +
107D LEU* 3.3 9.3 + - + +
108D TRP* 3.1 62.2 + - + +
249D PHE* 4.3 12.6 - - + -
286D TRP* 4.3 19.7 - - + -
288D ILE* 3.9 9.6 - - + -
331D PHE* 3.8 28.0 - - + -
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Residues in contact with ALA 105 (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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101D VAL 2.9 18.0 + - - +
102D ASN 3.6 4.3 - - - +
104D VAL* 1.3 76.3 - - - +
106D ASP* 1.3 61.8 + - - +
108D TRP* 3.1 4.9 + - - +
109D HIS 3.1 4.9 + - - -
110D ALA* 3.0 33.1 + - + +
118D ALA* 3.6 26.5 - - + -
288D ILE* 3.7 26.1 - - + +
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Residues in contact with ASP 106 (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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102D ASN 2.9 18.1 + - - +
103D MET 3.6 4.0 - - - +
104D VAL 3.2 0.2 - - - -
105D ALA* 1.3 76.8 - - - +
107D LEU* 1.3 62.5 + - - +
109D HIS* 3.0 20.0 + - - +
110D ALA 4.8 3.8 - - - +
336D ARG* 3.7 18.4 + - - -
30E LYS 3.7 11.6 - - - +
31E ARG* 3.5 27.3 + - - +
32E PHE* 3.0 21.2 + - - +
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Residues in contact with LEU 107 (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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103D MET 2.9 13.5 + - - +
104D VAL* 3.3 12.1 + - - +
106D ASP* 1.3 77.9 + - - +
108D TRP* 1.3 64.5 + - + +
109D HIS* 3.3 14.3 + - - -
248D GLY 4.0 11.9 - - - +
249D PHE* 3.9 27.4 - - + -
252D PRO* 3.7 26.5 - - + +
253D PHE* 3.6 41.7 - - + -
261D ASP* 4.5 1.2 - - - +
336D ARG* 3.9 24.2 + - - +
32E PHE* 4.0 21.1 - - + +
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Residues in contact with TRP 108 (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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104D VAL* 3.1 25.9 + - + +
105D ALA 3.1 2.7 + - - +
106D ASP 3.1 1.0 - - - -
107D LEU* 1.3 90.1 - - + +
109D HIS* 1.3 71.2 + - - +
110D ALA 3.4 1.8 - - - -
248D GLY* 2.9 26.6 + - - -
249D PHE* 4.5 4.3 - + - -
252D PRO* 4.1 2.0 - - + -
260D TRP* 3.6 24.4 - + - -
261D ASP* 3.3 7.6 - - + -
262D PHE* 3.1 29.1 + - + -
270D ILE* 3.3 56.3 - - + -
271D SER* 4.3 0.2 - - - -
272D ALA* 3.5 39.3 - - + -
286D TRP* 4.3 5.8 - - + -
288D ILE* 3.6 31.4 - - + -
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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