Contacts of the helix formed by residues 90 - 108 (chain F) 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 F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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53A ASP* 3.1 22.9 - - - +
54A GLY 3.6 24.5 - - - -
55A ASN* 4.7 1.9 - - - -
56A ALA* 3.2 23.9 - - + +
62A THR* 5.8 1.0 - - - +
66A THR* 4.3 5.2 - - - +
81F ASN* 3.2 19.3 + - + +
82F LYS* 3.8 28.9 - - + -
83F ASN* 3.4 37.2 - - + +
86F ASP* 3.0 24.9 + - + +
87F LYS* 3.5 4.1 - - - +
89F GLU* 1.3 97.6 - - + +
91F PRO* 1.3 62.0 - - - +
93F SER* 3.5 10.2 + - - -
94F ALA* 3.1 20.3 + - - +
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Residues in contact with PRO 91 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52A LEU* 3.9 17.7 - - + +
53A ASP* 3.8 2.2 - - - +
54A GLY 4.6 0.4 - - - +
87F LYS 3.2 15.2 - - - +
88F GLU 3.8 8.5 - - - +
89F GLU 3.2 11.7 - - - +
90F TYR* 1.3 89.8 - - - +
92F GLN* 1.3 61.3 + - - +
94F ALA* 3.5 6.2 + - + +
95F ALA* 2.9 27.2 + - - +
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Residues in contact with GLN 92 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49A GLU* 2.8 68.0 + - + +
50A LEU* 4.3 2.7 - - - +
52A LEU* 4.0 10.8 - - + +
53A ASP* 2.9 21.8 + - - +
436B LEU* 3.6 25.0 - - - +
91F PRO* 1.3 81.1 - - - +
93F SER* 1.3 64.7 + - - +
95F ALA* 3.1 13.6 + - - +
96F ILE* 3.0 31.6 + - + +
99F ARG* 3.7 10.7 - - - +
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Residues in contact with SER 93 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50A LEU* 4.1 1.2 - - - +
53A ASP* 2.6 27.2 + - - -
82F LYS* 3.5 16.6 - - - +
83F ASN 5.6 1.6 - - - -
84F TRP* 5.9 2.4 - - - -
90F TYR* 3.8 13.0 - - - -
92F GLN* 1.3 75.1 - - - +
94F ALA* 1.3 62.7 + - - +
96F ILE* 3.2 10.7 + - - +
97F ASP* 3.0 23.6 + - - +
321F ALA* 4.0 20.9 - - - +
324F VAL* 4.7 3.1 - - - +
325F ILE* 3.7 11.7 - - - +
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Residues in contact with ALA 94 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84F TRP* 5.7 2.0 - - - +
87F LYS* 4.0 38.4 - - + +
90F TYR 3.1 14.5 + - - +
91F PRO* 3.6 12.6 - - + +
93F SER* 1.3 76.9 - - - +
95F ALA* 1.3 63.3 + - - +
97F ASP* 3.2 9.1 + - - +
98F LEU* 3.0 28.4 + - + +
310F ILE* 6.0 0.9 - - + -
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Residues in contact with ALA 95 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91F PRO 2.9 17.8 + - - +
92F GLN* 3.1 23.1 + - - +
94F ALA* 1.3 73.5 - - - +
96F ILE* 1.3 63.2 + - - +
98F LEU* 3.2 10.6 + - - +
99F ARG* 3.0 35.7 + - - +
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Residues in contact with ILE 96 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46A ILE* 4.4 14.1 - - + -
49A GLU* 3.7 31.6 - - + +
50A LEU* 4.0 24.9 - - + -
92F GLN 3.0 20.0 + - - +
93F SER* 3.7 4.5 - - - +
94F ALA 3.2 0.2 - - - -
95F ALA* 1.3 75.5 - - - +
97F ASP* 1.3 66.4 + - - +
99F ARG* 3.0 25.7 + - - +
100F CYS* 3.0 13.0 + - - -
324F VAL* 4.2 13.9 - - + +
325F ILE* 4.3 9.6 - - + -
328F TYR* 3.5 35.4 - - + -
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Residues in contact with ASP 97 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84F TRP* 3.0 35.0 + - + +
87F LYS* 4.6 6.8 + - - +
93F SER 3.0 12.9 + - - +
94F ALA* 3.4 11.9 - - - +
96F ILE* 1.3 77.8 - - - +
98F LEU* 1.3 68.3 + - + +
100F CYS* 3.1 6.3 + - - +
101F VAL* 3.0 28.4 + - - +
121F THR* 5.9 0.2 - - - -
122F ASN* 3.2 26.0 + - - +
286F TRP* 3.7 6.8 - - - -
324F VAL* 3.5 20.0 - - + +
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Residues in contact with LEU 98 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87F LYS* 6.5 1.1 - - - -
94F ALA* 3.0 21.2 + - + +
95F ALA* 3.2 10.3 + - - +
97F ASP* 1.3 81.7 - - - +
99F ARG* 1.3 63.4 + - - +
101F VAL* 3.3 8.0 + - + +
102F ASN* 3.2 14.8 + - - -
117F GLN* 3.1 50.8 + - + +
310F ILE* 6.3 8.1 - - + -
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Residues in contact with ARG 99 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25A THR* 3.4 25.4 + - - -
26A ILE* 4.1 17.2 - - - +
29A SER* 3.7 37.0 - - - +
49A GLU* 2.7 32.0 + - - -
92F GLN* 3.7 11.2 - - - +
95F ALA* 3.0 23.0 + - - +
96F ILE* 3.0 15.0 + - - +
98F LEU* 1.3 74.5 - - - +
100F CYS* 1.3 59.9 + - - +
102F ASN* 3.1 6.5 + - - +
103F MET* 2.8 37.5 + - + +
328F TYR* 2.9 45.1 + - + -
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Residues in contact with CYS 100 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96F ILE* 3.0 18.2 + - - -
97F ASP 3.1 4.9 + - - +
99F ARG* 1.3 76.3 - - - +
101F VAL* 1.3 56.7 + - - +
103F MET* 3.1 7.9 + - - +
104F VAL* 2.8 35.2 + - - +
286F TRP* 3.4 31.9 - - + -
324F VAL* 3.9 13.2 - - - -
327F GLN* 4.5 0.2 - - - -
328F TYR* 3.8 36.8 - - - -
331F PHE* 4.3 11.7 - - + -
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Residues in contact with VAL 101 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97F ASP* 3.0 24.7 + - - +
98F LEU* 3.7 12.6 - - + +
99F ARG 3.2 0.4 - - - -
100F CYS* 1.3 73.5 - - - +
102F ASN* 1.3 58.1 + - - +
104F VAL* 4.9 0.9 - - - -
105F ALA* 2.9 31.4 + - - +
117F GLN* 4.2 4.7 - - - +
118F ALA* 3.9 16.8 - - + +
120F GLY* 3.8 46.2 - - - +
121F THR* 4.3 5.8 - - - +
122F ASN 4.3 1.6 - - - +
286F TRP* 3.9 20.4 - - + -
288F ILE* 3.8 12.9 - - + +
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Residues in contact with ASN 102 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29A SER* 3.9 13.8 + - - +
30A LYS* 3.6 27.9 - - - +
98F LEU 3.2 9.4 + - - -
99F ARG* 3.1 8.7 + - - +
101F VAL* 1.3 75.5 - - - +
103F MET* 1.3 58.4 + - - +
105F ALA* 3.4 2.1 + - - +
106F ASP* 2.9 29.8 + - - +
113F PRO* 5.0 1.4 - - - +
116F GLY 3.5 14.5 + - - +
117F GLN* 3.1 23.4 + - - +
118F ALA* 2.6 37.5 + - - +
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Residues in contact with MET 103 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25A THR 5.6 0.9 - - - +
28A GLU 4.3 10.8 - - - +
29A SER* 4.4 14.4 - - - +
31A ARG 3.3 25.6 - - - +
32A PHE* 3.6 25.8 - - + +
33A PRO* 3.9 25.4 - - + -
99F ARG* 2.8 20.1 + - + +
100F CYS 3.1 6.7 + - - +
102F ASN* 1.3 74.3 - - - +
104F VAL* 1.3 66.8 + - - +
106F ASP* 3.3 3.3 + - - +
107F LEU* 2.9 22.7 + - - +
328F TYR* 3.9 28.3 - - + +
331F PHE* 3.9 24.5 - - + -
332F LEU* 5.2 3.1 - - + -
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Residues in contact with VAL 104 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32A PHE* 4.9 0.2 - - - -
100F CYS 2.8 22.6 + - - +
101F VAL* 4.1 2.5 - - - +
103F MET* 1.3 71.9 - - - +
105F ALA* 1.3 63.5 + - - +
107F LEU* 3.0 18.3 + - + +
108F TRP* 3.1 55.5 + - + -
249F PHE* 4.1 14.1 - - + -
286F TRP* 4.3 20.4 - - + -
288F ILE* 3.9 11.0 - - + -
331F PHE* 3.8 27.1 - - + -
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Residues in contact with ALA 105 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101F VAL 2.9 19.7 + - - +
102F ASN 3.5 2.9 - - - +
104F VAL* 1.3 76.1 - - - +
106F ASP* 1.3 62.3 + - - +
108F TRP* 3.0 13.1 + - - +
110F ALA* 3.1 30.7 + - + +
118F ALA* 3.3 25.8 - - + -
288F ILE* 3.9 24.5 - - + +
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Residues in contact with ASP 106 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30A LYS 4.1 2.9 - - - +
31A ARG* 3.2 24.0 - - - +
32A PHE 3.0 23.1 + - - +
102F ASN 2.9 17.1 + - - +
103F MET 3.5 4.0 - - - +
104F VAL 3.2 0.2 - - - -
105F ALA* 1.3 76.3 - - - +
107F LEU* 1.3 62.4 + - - +
109F HIS* 3.1 17.9 + - - +
110F ALA 4.9 4.0 - - - +
336F ARG* 3.6 20.0 + - - -
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Residues in contact with LEU 107 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32A PHE* 3.9 26.7 - - + -
103F MET 2.9 13.0 + - - +
104F VAL* 3.2 13.5 - - - +
106F ASP* 1.3 78.1 + - - +
108F TRP* 1.3 71.3 + - + +
109F HIS* 3.4 11.9 + - - -
248F GLY 4.2 3.8 - - - +
249F PHE* 3.9 31.4 - - + -
252F PRO* 3.8 23.7 - - + +
253F PHE* 3.6 31.9 - - + -
261F ASP* 4.3 1.6 - - - +
336F ARG* 3.8 24.0 + - - +
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Residues in contact with TRP 108 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104F VAL* 3.1 23.5 + - + -
105F ALA 3.0 6.4 + - - +
107F LEU* 1.3 94.2 - - + +
109F HIS* 1.3 70.1 + - - +
110F ALA 3.2 3.0 + - - -
248F GLY* 3.1 27.8 + - - -
249F PHE* 4.6 4.3 - + - -
252F PRO* 4.3 1.1 - - + -
260F TRP* 3.6 24.8 - + - -
261F ASP* 3.3 4.9 - - + +
262F PHE* 3.1 35.0 + - + -
270F ILE* 3.5 43.7 - - + -
271F SER* 4.6 0.2 - - - -
272F ALA* 3.4 39.0 - - + -
286F TRP* 4.6 5.6 - - + -
288F ILE* 3.5 35.2 - - + -
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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