Contacts of the strand formed by residues 76 - 93 (chain F) in PDB entry 2IFG
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 TRP 76 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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12E PHE* 3.9 23.8 - + - -
69E ARG* 5.2 7.9 - - + -
70E GLY* 3.8 31.7 - - - -
71F ILE* 4.0 14.2 - - + +
72F ASP* 2.9 26.2 + - + +
73F SER* 3.7 19.1 + - - +
74F LYS 3.7 2.0 - - - -
75F HIS* 1.3 96.6 + - + +
77F ASN* 1.3 67.5 + - - +
78F SER* 3.9 1.4 + - - -
112F LEU* 4.3 16.4 - - + -
113F SER 3.4 11.7 - - - +
114F ARG* 3.3 68.4 - - + -
115F LYS* 3.7 9.4 + - - +
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Residues in contact with ASN 77 (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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76F TRP* 1.3 77.3 - - - +
78F SER* 1.3 65.7 + - - +
113F SER* 2.7 44.1 + - - +
114F ARG 5.0 0.7 - - - -
115F LYS* 2.8 45.8 - - - +
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Residues in contact with SER 78 (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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67F GLY* 2.9 22.8 + - - -
68F CYS* 3.5 23.2 + - - -
71F ILE* 3.7 23.5 - - - +
76F TRP* 4.2 1.4 + - - -
77F ASN* 1.3 80.0 - - - +
79F TYR* 1.3 71.1 + - - +
110F CYS* 4.1 5.2 - - - -
111F VAL 3.2 15.0 - - - -
112F LEU* 4.7 2.5 - - - -
113F SER* 5.4 0.7 - - - -
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Residues in contact with TYR 79 (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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297A HIS* 4.7 5.5 + - - -
347A ARG* 5.4 1.7 + - - -
11E GLU* 3.3 25.6 + - - -
67F GLY* 4.0 11.0 - - - +
68F CYS* 3.2 10.2 - - - -
78F SER* 1.3 83.1 - - - +
80F CYS* 1.3 70.1 + - - +
81F THR* 4.0 12.5 - - - +
111F VAL* 2.9 69.1 + - + +
113F SER* 5.9 2.5 - - - -
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Residues in contact with CYS 80 (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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14F VAL 4.0 0.7 - - - -
15F CYS* 2.0 50.7 - - - -
16F ASP 4.9 1.3 - - - +
58F CYS* 3.8 7.0 - - + +
67F GLY 4.8 2.8 - - - -
68F CYS* 3.7 19.1 - - - -
79F TYR* 1.3 81.8 - - - +
81F THR* 1.3 64.3 + - - +
108F CYS* 3.7 12.6 - - - -
109F VAL 3.4 3.8 - - - -
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Residues in contact with THR 81 (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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297A HIS* 4.0 16.8 - - + +
58F CYS* 3.0 8.9 - - - -
79F TYR* 4.0 14.0 - - + +
80F CYS* 1.3 77.4 - - - +
82F THR* 1.3 67.9 + - - +
83F THR* 3.6 4.1 + - + -
108F CYS* 3.1 0.3 - - - -
109F VAL* 2.7 47.0 + - + +
111F VAL* 3.4 27.8 - - + -
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Residues in contact with THR 82 (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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56F THR 3.7 4.5 - - - +
57F LYS* 3.6 24.7 - - + +
58F CYS* 3.2 22.1 + - - +
81F THR* 1.3 81.5 + - - +
83F THR* 1.3 62.0 + - - +
84F HIS* 3.5 17.5 - - - -
105F ASP* 3.5 26.5 - - + +
107F ALA 3.3 15.3 - - - +
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Residues in contact with THR 83 (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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297A HIS* 4.7 11.2 - - + -
350A GLN* 4.4 13.9 - - - +
106E THR 5.5 0.2 + - - -
107E ALA* 4.8 3.3 - - - +
81F THR* 4.1 1.8 - - + +
82F THR* 1.3 76.4 - - - +
84F HIS* 1.3 66.3 + - - +
105F ASP* 3.8 3.3 - - - -
106F THR* 2.9 23.8 + - - +
107F ALA* 2.7 33.8 + - - +
109F VAL* 3.3 38.4 - - + +
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Residues in contact with HIS 84 (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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327A PHE* 4.5 11.8 - + - -
349A ASN* 4.7 7.3 + - - -
350A GLN* 3.2 26.9 + - - +
54E PHE* 4.7 2.3 - - - -
56E THR* 5.3 0.9 + - - -
106E THR 4.7 2.9 - - - +
82F THR* 3.5 21.8 + - - +
83F THR* 1.3 76.1 - - - +
85F THR* 1.3 60.9 + - - +
86F PHE* 6.1 1.1 - - + -
103F ARG* 2.7 51.9 + - + +
104F ILE* 3.1 11.9 - - - +
105F ASP* 3.4 32.9 + - - -
106F THR* 3.2 13.8 - - - +
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Residues in contact with THR 85 (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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54E PHE* 3.6 28.0 + - - -
56E THR* 5.4 1.1 + - - -
85E THR* 4.9 9.9 - - + +
106E THR* 3.5 22.3 + - - +
54F PHE 6.0 0.2 - - - +
84F HIS* 1.3 76.5 - - - +
86F PHE* 1.3 69.5 + - - +
87F VAL* 3.7 14.6 - - + +
102F ILE 3.6 0.5 - - - +
103F ARG* 3.6 3.5 - - - -
104F ILE* 2.9 50.1 + - + +
105F ASP 5.0 0.4 - - - +
106F THR* 3.6 14.1 - - - +
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Residues in contact with PHE 86 (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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350A GLN* 4.0 22.4 - - + -
352A THR* 4.0 6.1 - - + -
21E TRP* 4.6 1.1 - - + -
54E PHE* 3.4 56.7 + + + +
30F ASP 4.2 13.2 - - - -
31F ILE* 3.6 38.8 - - + -
84F HIS* 6.3 0.9 - - + -
85F THR* 1.3 75.6 + - - +
87F VAL* 1.3 66.8 + - - +
101F PHE* 4.0 14.4 - - + -
102F ILE* 3.1 19.1 - - - -
103F ARG* 3.5 47.1 - - + -
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Residues in contact with VAL 87 (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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87E VAL* 3.6 46.4 - - + -
88E LYS* 5.3 2.9 - - + +
53F PHE* 4.8 11.2 - - + -
85F THR* 3.7 9.8 + - + +
86F PHE* 1.3 80.8 - - - +
88F LYS* 1.3 77.0 + - + +
101F PHE* 3.5 7.1 - - - -
102F ILE* 2.8 38.2 + - + +
104F ILE* 3.4 31.6 - - + +
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Residues in contact with LYS 88 (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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49E PHE* 4.4 12.5 - - - +
50E LYS 5.7 2.6 + - - -
52E TYR* 5.9 1.8 - - - +
51F GLN* 4.6 0.7 - - - +
53F PHE* 4.4 4.5 - - - -
87F VAL* 1.3 88.0 - - + +
89F ALA* 1.3 62.0 + - - +
99F TRP* 2.8 69.1 + - + +
100F ARG* 3.6 4.7 - - - +
101F PHE* 3.3 57.4 - - + +
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Residues in contact with ALA 89 (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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38F VAL* 4.8 1.1 - - + -
51F GLN* 3.3 13.9 - - - +
53F PHE* 3.8 10.3 - - + -
88F LYS* 1.3 79.0 - - - +
90F LEU* 1.3 64.3 + - - +
91F THR* 3.2 9.4 + - + +
99F TRP* 3.5 7.8 - - - -
100F ARG 2.7 34.7 + - - +
102F ILE* 3.4 33.7 - - + -
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Residues in contact with LEU 90 (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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44E ILE* 5.0 13.2 - - + -
38F VAL* 3.9 3.1 - - - +
39F LEU* 2.9 40.2 + - + +
41F GLU 3.6 16.8 - - - +
42F VAL* 3.5 25.4 - - + -
43F ASN 4.6 2.2 - - - +
51F GLN* 2.9 22.9 + - - +
89F ALA* 1.3 69.5 - - - +
91F THR* 1.3 60.5 + - - +
97F ALA* 4.8 10.1 - - + -
98F ALA* 3.2 22.2 - - - +
99F TRP* 3.1 23.7 - - + +
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Residues in contact with THR 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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36F VAL* 3.9 16.5 - - + +
37F MET 2.8 18.4 - - - +
38F VAL* 4.4 4.7 - - + -
39F LEU* 3.2 11.0 - - - +
89F ALA* 3.5 14.1 - - + +
90F LEU* 1.3 78.0 - - - +
92F MET* 1.3 60.8 + - - +
93F ASP* 6.0 0.3 - - - +
97F ALA* 3.1 7.4 - - - -
98F ALA* 2.8 28.1 + - - +
100F ARG* 3.0 29.8 - - + +
102F ILE* 3.8 28.5 - - + -
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Residues in contact with MET 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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36F VAL* 4.0 6.4 - - - +
37F MET* 2.6 62.2 + - + +
39F LEU* 3.8 25.1 - - + -
91F THR* 1.3 79.2 - - - +
93F ASP* 1.3 59.7 - - - +
94F GLY 3.5 19.7 - - - +
95F LYS* 4.4 7.9 - - - -
96F GLN 3.4 5.4 - - - +
97F ALA* 3.2 38.1 - - + +
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Residues in contact with ASP 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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34F LYS* 3.9 22.9 + - + +
36F VAL* 4.9 12.6 - - + -
37F MET* 5.5 0.2 - - - -
91F THR* 6.0 0.4 - - - +
92F MET* 1.3 73.6 - - - +
94F GLY* 1.3 58.6 + - - +
95F LYS* 4.7 0.7 - - - -
96F GLN* 3.0 38.3 + - - +
98F ALA* 6.4 0.4 - - + -
100F ARG* 5.6 11.3 + - - +
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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