Contacts of the helix formed by residues 90 - 108 (chain E) 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 E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53D ASP* 3.1 22.4 - - + +
54D GLY 3.4 26.9 - - - -
55D ASN 4.4 2.7 + - - -
56D ALA* 3.3 23.4 - - + +
62D THR* 5.9 0.5 - - - +
66D THR* 4.3 5.2 - - - +
81E ASN* 3.1 19.7 + - + +
82E LYS* 3.8 26.5 - - + -
83E ASN* 3.4 38.3 - - + +
86E ASP* 3.0 23.9 + - + +
87E LYS* 3.6 4.7 - - - +
89E GLU* 1.3 98.1 - - + +
91E PRO* 1.4 60.6 - - - +
93E SER* 3.5 11.5 + - - +
94E ALA* 3.2 18.4 + - - +
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Residues in contact with PRO 91 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52D LEU* 3.9 18.8 - - + +
53D ASP* 3.9 3.1 - - - +
54D GLY 4.6 0.2 - - - +
87E LYS 3.1 16.2 - - - +
88E GLU* 3.6 9.9 - - - +
89E GLU 3.1 14.8 - - - +
90E TYR* 1.4 85.8 - - - +
92E GLN* 1.3 59.0 + - - +
94E ALA* 3.3 7.1 - - + +
95E ALA* 3.1 23.6 + - - +
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Residues in contact with GLN 92 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
436C LEU* 4.8 5.4 - - - +
49D GLU* 2.8 64.2 + - + +
50D LEU* 4.6 1.3 - - - -
52D LEU* 3.4 31.5 - - + +
53D ASP* 3.1 14.0 + - - +
91E PRO* 1.3 78.0 - - - +
93E SER* 1.3 66.3 + - - +
94E ALA 3.2 0.4 - - - -
95E ALA* 3.2 10.8 + - - +
96E ILE* 2.9 29.7 + - + +
99E ARG* 3.6 12.7 - - - +
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Residues in contact with SER 93 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50D LEU* 4.2 1.6 - - - +
53D ASP* 2.8 24.6 + - - -
82E LYS* 3.4 17.2 - - - +
83E ASN 5.8 0.9 - - - -
84E TRP* 6.0 2.0 - - - -
90E TYR* 3.8 14.4 - - - -
92E GLN* 1.3 75.6 - - - +
94E ALA* 1.3 64.8 + - - +
96E ILE* 3.0 12.7 + - - +
97E ASP* 3.0 21.6 + - - +
321E ALA* 3.9 22.5 - - - +
324E VAL* 5.0 2.8 - - - +
325E ILE* 3.7 9.8 - - - +
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Residues in contact with ALA 94 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84E TRP* 5.8 0.7 - - - -
87E LYS* 3.8 39.4 - - + +
90E TYR 3.2 11.5 + - - +
91E PRO* 3.3 13.5 - - + +
92E GLN 3.2 0.2 - - - -
93E SER* 1.3 77.8 - - - +
95E ALA* 1.3 56.0 + - - +
97E ASP* 3.2 9.7 - - - +
98E LEU* 3.0 36.0 + - + +
310E ILE* 5.8 1.8 - - + -
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Residues in contact with ALA 95 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91E PRO 3.1 14.3 + - - +
92E GLN* 3.2 26.2 + - - +
94E ALA* 1.3 75.8 - - - +
96E ILE* 1.3 62.7 + - - +
98E LEU* 3.3 10.5 + - - +
99E ARG* 3.1 33.5 + - - +
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Residues in contact with ILE 96 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46D ILE* 4.3 16.8 - - + -
49D GLU* 3.7 30.3 - - + +
50D LEU* 3.8 26.5 - - + -
92E GLN* 2.9 22.2 + - + +
93E SER* 3.0 4.9 + - - +
95E ALA* 1.3 77.6 - - - +
97E ASP* 1.3 62.4 + - - +
99E ARG* 3.1 18.8 + - - +
100E CYS* 3.0 21.1 + - - -
324E VAL* 4.3 11.2 - - + -
325E ILE* 4.4 11.4 - - + -
328E TYR* 3.5 34.0 - - + -
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Residues in contact with ASP 97 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84E TRP* 2.8 38.0 + - + +
87E LYS* 4.3 8.8 + - - -
93E SER 3.0 12.2 + - - +
94E ALA* 3.2 13.5 - - - +
96E ILE* 1.3 73.9 - - - +
98E LEU* 1.3 70.4 + - - +
100E CYS* 3.0 12.9 + - - +
101E VAL* 3.1 17.4 + - - +
122E ASN* 3.3 24.8 + - - +
286E TRP* 3.9 7.6 - - - -
324E VAL* 3.7 16.2 - - + +
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Residues in contact with LEU 98 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94E ALA* 3.0 24.2 + - + +
95E ALA* 3.8 7.9 - - - +
96E ILE 3.3 0.2 - - - -
97E ASP* 1.3 82.5 - - + +
99E ARG* 1.3 63.5 + - - +
101E VAL* 3.2 10.0 + - + -
102E ASN* 3.0 20.8 + - - -
117E GLN* 3.4 43.4 + - + +
310E ILE* 5.6 15.0 - - + -
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Residues in contact with ARG 99 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25D THR* 3.4 24.5 + - - -
26D ILE* 4.1 18.2 - - - +
29D SER* 4.0 34.4 - - - +
49D GLU* 2.6 31.0 + - - -
92E GLN* 3.6 12.6 - - - +
95E ALA* 3.1 23.3 + - - +
96E ILE* 3.1 15.0 + - - +
98E LEU* 1.3 76.6 - - - +
100E CYS* 1.3 62.7 + - - +
102E ASN* 3.2 6.8 + - - +
103E MET* 2.9 30.8 + - + +
328E TYR* 3.0 46.8 + - + -
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Residues in contact with CYS 100 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96E ILE 3.0 19.6 + - - -
97E ASP 3.0 4.0 + - - +
99E ARG* 1.3 76.8 - - - +
101E VAL* 1.3 51.1 + - - +
103E MET* 3.1 4.4 + - - +
104E VAL* 2.8 39.8 + - - +
286E TRP* 3.2 33.7 - - + -
324E VAL* 4.0 9.2 - - - -
327E GLN* 4.4 1.3 - - - -
328E TYR* 3.6 43.3 - - - -
331E PHE* 4.1 14.8 - - + -
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Residues in contact with VAL 101 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97E ASP* 3.1 19.7 + - - +
98E LEU* 3.5 14.4 - - + +
100E CYS* 1.3 74.5 - - - +
102E ASN* 1.3 58.7 + - - +
105E ALA* 2.9 28.8 + - - +
117E GLN* 4.2 6.1 - - - +
118E ALA* 3.9 24.9 - - + +
120E GLY* 3.9 32.5 - - - +
121E THR* 4.2 9.9 - - - +
122E ASN 4.4 1.1 - - - +
286E TRP* 3.9 18.6 - - + -
288E ILE* 3.4 12.3 - - + +
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Residues in contact with ASN 102 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29D SER 4.4 2.7 + - - +
30D LYS* 3.5 45.0 - - + +
98E LEU 3.0 11.7 + - - -
99E ARG* 3.2 6.3 + - - +
101E VAL* 1.3 75.9 - - - +
103E MET* 1.3 58.5 + - - +
105E ALA* 3.6 1.2 - - - +
106E ASP* 2.8 30.8 + - - +
113E PRO* 4.7 2.1 - - - +
116E GLY 3.8 5.3 + - - +
117E GLN* 3.1 29.5 + - - +
118E ALA* 2.7 38.6 + - - +
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Residues in contact with MET 103 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25D THR 5.6 0.7 - - - +
28D GLU 4.7 0.9 - - - +
29D SER* 4.1 24.7 - - - +
30D LYS 4.3 0.7 - - - +
31D ARG 3.5 25.1 - - - +
32D PHE* 3.6 25.5 - - + +
33D PRO* 3.8 25.4 - - + -
99E ARG* 2.9 20.8 + - + +
100E CYS 3.5 4.3 - - - +
102E ASN* 1.3 74.0 - - - +
104E VAL* 1.3 62.0 + - - +
106E ASP* 3.4 1.7 + - - +
107E LEU* 2.9 29.1 + - - +
328E TYR* 3.8 28.9 - - + +
331E PHE* 3.9 24.7 - - + -
332E LEU* 5.4 2.5 - - + -
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Residues in contact with VAL 104 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32D PHE* 5.1 0.4 - - + -
100E CYS 2.8 20.5 + - - +
101E VAL* 4.0 2.9 - - - +
103E MET* 1.3 76.6 - - - +
105E ALA* 1.3 63.1 + - - +
107E LEU* 3.2 10.6 + - - +
108E TRP* 3.1 62.9 + - + -
249E PHE* 4.1 11.4 - - + -
286E TRP* 4.1 24.7 - - + -
288E ILE* 3.8 10.5 - - + -
331E PHE* 3.7 27.1 - - + -
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Residues in contact with ALA 105 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101E VAL 2.9 18.3 + - - +
102E ASN 3.6 2.9 - - - +
104E VAL* 1.3 74.3 - - - +
106E ASP* 1.3 62.8 + - - +
108E TRP* 3.0 12.4 + - - +
110E ALA* 3.1 30.6 + - + +
118E ALA* 3.5 25.8 - - + -
288E ILE* 3.7 26.5 - - + +
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Residues in contact with ASP 106 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30D LYS 3.9 9.4 - - - +
31D ARG* 3.4 14.2 - - - +
32D PHE* 2.8 26.2 + - - +
102E ASN 2.8 21.0 + - - +
103E MET 3.7 2.9 - - - +
105E ALA* 1.3 69.6 - - - +
107E LEU* 1.3 67.8 + - - +
109E HIS* 2.9 19.4 + - - +
110E ALA 4.9 4.0 - - - +
336E ARG* 3.5 21.4 + - - -
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Residues in contact with LEU 107 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32D PHE* 3.9 25.1 - - + +
103E MET 2.9 13.4 + - - +
104E VAL* 3.3 11.4 - - - +
106E ASP* 1.3 78.2 + - - +
108E TRP* 1.3 75.9 + - + +
109E HIS* 3.5 15.4 + - - -
248E GLY 4.1 8.3 - - - +
249E PHE* 4.2 12.6 - - + -
252E PRO* 3.9 22.6 - - + +
253E PHE* 3.6 42.2 - - + -
261E ASP* 4.6 1.4 - - - +
336E ARG* 3.8 27.1 + - - +
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Residues in contact with TRP 108 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104E VAL* 3.1 31.6 + - + +
105E ALA 3.0 5.1 + - - +
106E ASP 2.9 1.4 + - - -
107E LEU* 1.3 92.8 - - + +
109E HIS* 1.3 67.5 + - - +
110E ALA 3.2 2.0 - - - -
248E GLY* 2.8 28.5 + - - -
249E PHE* 4.5 4.7 - + - -
252E PRO* 4.3 0.9 - - + -
260E TRP* 3.7 19.2 - + - -
261E ASP* 3.4 7.2 - - + +
262E PHE* 3.1 35.0 + + + -
270E ILE* 3.2 55.6 - - + -
271E SER* 4.4 0.2 - - - -
272E ALA* 3.4 39.5 - - + -
286E TRP* 4.6 5.8 - - + -
288E ILE* 3.7 23.6 - - + -
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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