Contacts of the strand formed by residues 96 - 114 (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 GLN 96 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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91F THR 4.4 0.2 - - - -
92F MET* 3.4 4.0 - - - -
93F ASP* 3.0 47.5 + - + +
94F GLY 2.9 4.9 + - - -
95F LYS* 1.3 118.5 + - + +
97F ALA* 1.3 68.7 + - - +
98F ALA* 3.4 8.8 + - + +
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Residues in contact with ALA 97 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39F LEU* 5.1 3.8 - - + -
90F LEU* 4.8 15.3 - - + -
91F THR 3.1 10.8 - - - +
92F MET* 3.2 18.3 - - + -
95F LYS 3.7 3.6 + - - -
96F GLN* 1.3 75.2 + - - +
98F ALA* 1.3 60.1 + - - +
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Residues in contact with ALA 98 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89F ALA 3.3 1.4 - - - +
90F LEU* 3.2 11.0 - - - +
91F THR* 2.8 34.6 + - - +
93F ASP* 6.4 0.7 - - + -
96F GLN* 3.4 10.4 + - + +
97F ALA* 1.3 75.5 - - - +
99F TRP* 1.3 62.1 + - - +
100F ARG* 3.4 35.6 + - - +
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Residues in contact with TRP 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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42E VAL* 4.9 10.9 - - + +
44E ILE* 3.3 27.7 - - + +
49E PHE* 3.6 45.4 - + + -
99E TRP* 3.5 37.0 - + - -
42F VAL* 3.8 20.4 - - + -
44F ILE* 5.3 1.3 - - + -
51F GLN* 3.9 7.4 - - - -
88F LYS* 2.8 53.3 + - + +
89F ALA* 3.5 5.2 - - - -
90F LEU* 3.1 50.0 - - + +
98F ALA* 1.3 71.9 - - - +
100F ARG* 1.3 64.4 + - - +
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Residues in contact with ARG 100 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30F ASP* 5.0 13.0 - - + -
32F LYS* 3.5 29.2 - - - +
36F VAL* 6.0 4.0 - - + -
88F LYS* 3.6 5.6 - - - +
89F ALA* 2.7 38.0 + - - +
91F THR* 3.0 27.4 - - + +
93F ASP* 5.6 11.6 + - - +
98F ALA* 3.5 25.1 - - + +
99F TRP* 1.3 78.2 + - - +
101F PHE* 1.3 64.1 + - - +
102F ILE* 3.6 3.0 + - + +
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Residues in contact with PHE 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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21E TRP* 3.3 40.4 - + + -
52E TYR* 3.7 31.6 - + + -
53E PHE* 5.3 0.2 - - - -
54E PHE 5.0 2.0 - - - -
30F ASP* 3.3 8.0 - - - +
31F ILE* 3.2 37.7 + - + +
86F PHE* 4.0 17.7 - - + -
87F VAL* 3.4 11.0 - - - -
88F LYS* 3.3 59.3 - - + +
100F ARG* 1.3 72.4 - - - +
102F ILE* 1.3 60.0 + - - +
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Residues in contact with ILE 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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25F LYS* 4.6 1.3 - - + -
28F ALA* 3.9 26.5 - - + -
29F THR 3.5 10.3 - - - +
30F ASP* 4.6 1.3 - - + -
36F VAL* 4.3 8.3 - - + -
38F VAL* 4.4 6.3 - - + -
53F PHE* 3.9 19.5 - - + -
85F THR 3.6 0.3 - - - +
86F PHE* 3.1 11.6 - - - -
87F VAL* 2.8 43.0 + - + +
89F ALA* 3.4 21.8 - - + -
91F THR* 3.8 25.8 - - + -
100F ARG* 4.0 2.5 - - + +
101F PHE* 1.3 80.0 - - - +
103F ARG* 1.3 59.6 + - - +
104F ILE* 3.8 17.5 + - + +
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Residues in contact with ARG 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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327A PHE* 3.2 51.6 - - - +
349A ASN* 2.5 36.6 + - - -
350A GLN* 3.4 21.9 + - - +
25F LYS* 5.6 0.5 - - - -
28F ALA* 4.6 8.0 - - - +
29F THR* 3.0 24.8 + - - +
84F HIS* 2.7 59.1 + - + +
85F THR 3.6 3.4 - - - +
86F PHE* 3.5 27.5 - - + -
102F ILE* 1.3 74.3 - - - +
104F ILE* 1.3 65.6 + - - +
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Residues in contact with ILE 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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87E VAL* 5.8 0.4 - - + -
25F LYS* 4.2 13.0 - - + +
53F PHE* 4.5 14.6 - - + -
54F PHE 4.5 15.0 - - - +
55F GLU* 3.4 22.7 - - - +
84F HIS* 3.1 8.1 - - - +
85F THR* 2.9 44.0 + - + +
87F VAL* 3.4 36.8 - - + -
102F ILE* 4.2 20.0 - - + +
103F ARG* 1.3 80.5 - - - +
105F ASP* 1.3 67.4 + - - +
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Residues in contact with ASP 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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54F PHE 3.9 4.2 - - - +
55F GLU* 3.3 32.6 - - + +
56F THR 3.2 32.5 + - - +
57F LYS* 4.3 14.4 + - + +
82F THR* 3.5 17.3 - - + +
83F THR 3.8 4.9 - - - -
84F HIS* 3.4 20.7 + - - -
85F THR* 5.0 0.2 - - - +
104F ILE* 1.3 76.0 - - - +
106F THR* 1.3 57.9 + - - +
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Residues in contact with THR 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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350B GLN* 5.5 1.2 + - - -
83E THR* 5.3 0.5 + - - -
84E HIS 4.6 2.9 - - - +
85E THR* 3.5 13.4 - - - -
106E THR* 2.5 50.3 + - - +
55F GLU* 5.3 0.2 - - - +
56F THR* 3.3 22.4 + - - +
83F THR* 2.9 14.4 + - - +
84F HIS 3.2 30.5 - - - +
85F THR* 3.6 13.6 - - - -
105F ASP* 1.3 74.4 - - - +
107F ALA* 1.3 66.6 - - + +
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Residues in contact with ALA 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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83E THR* 4.9 4.3 - - - +
107E ALA* 3.7 26.0 - - + -
109E VAL* 5.1 4.3 - - + -
56F THR* 3.4 16.1 + - - -
82F THR* 3.3 10.4 - - - +
83F THR* 2.7 42.4 + - - +
106F THR* 1.3 80.1 - - - +
108F CYS* 1.3 60.7 + - - +
109F VAL* 4.6 2.9 - - + -
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Residues in contact with CYS 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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109E VAL* 4.5 9.7 - - - +
14F VAL* 5.6 1.2 - - - +
15F CYS* 3.7 30.6 - - + +
16F ASP 4.0 4.3 - - - +
17F SER* 4.1 18.7 - - - -
58F CYS* 2.0 60.1 - - - +
80F CYS* 3.7 9.6 - - - -
81F THR 3.1 4.5 - - - -
107F ALA* 1.3 76.3 - - - +
109F VAL* 1.3 62.9 + - - +
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Residues in contact with VAL 109 (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* 4.2 12.8 - - + +
13E SER* 6.5 0.4 - - - -
14E VAL* 5.8 2.7 - - + -
107E ALA* 5.2 4.5 - - + -
108E CYS 4.5 16.6 - - - +
109E VAL* 4.5 10.8 - - + -
14F VAL* 5.8 2.0 - - - -
15F CYS* 3.7 5.8 - - - -
80F CYS* 3.4 1.0 - - - -
81F THR* 2.7 51.1 + - + +
83F THR* 3.3 36.3 - - + +
107F ALA* 4.2 2.9 - - + -
108F CYS* 1.3 80.1 - - - +
110F CYS* 1.3 66.1 + - - +
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Residues in contact with CYS 110 (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* 5.4 0.5 + - - -
13E SER* 4.2 4.3 - - - -
14E VAL* 3.8 35.2 + - + +
14F VAL* 3.9 13.2 - - + +
15F CYS* 3.6 9.0 - - - -
68F CYS* 2.0 52.0 - - + -
71F ILE* 3.9 17.5 - - - -
78F SER* 4.1 4.9 - - - -
79F TYR 3.5 0.2 - - - -
109F VAL* 1.3 77.8 - - - +
111F VAL* 1.3 62.3 + - - +
112F LEU* 3.9 11.8 + - - -
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Residues in contact with VAL 111 (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* 3.6 23.3 - - + -
11E GLU* 3.6 27.8 - - + +
12E PHE 3.7 5.8 - - - +
78F SER* 3.2 26.9 - - - -
79F TYR* 2.9 52.1 + - + +
81F THR* 3.4 32.5 - - + -
109F VAL* 4.8 0.2 - - + -
110F CYS* 1.3 73.4 - - - +
112F LEU* 1.3 63.2 + - - +
113F SER* 5.1 0.2 - - - -
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Residues in contact with LEU 112 (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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10E GLY 3.8 0.5 - - - +
11E GLU* 3.2 8.3 - - - +
12E PHE* 2.7 45.6 + - + +
14E VAL* 3.3 37.9 - - + +
69E ARG* 3.2 51.1 - - + +
70E GLY* 3.6 11.4 - - - +
71F ILE* 5.4 4.5 - - + -
76F TRP* 4.3 19.3 - - + -
77F ASN 4.1 3.4 - - - +
78F SER* 4.7 2.7 - - - -
110F CYS* 3.9 15.7 - - - +
111F VAL* 1.3 74.5 - - - +
113F SER* 1.3 61.8 + - - +
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Residues in contact with SER 113 (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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9E ARG 4.9 5.0 + - - -
10E GLY 4.2 7.4 + - - -
11E GLU* 4.4 19.7 - - - +
76F TRP* 3.4 8.3 - - - -
77F ASN* 2.7 54.1 + - - +
78F SER* 5.4 0.4 - - - -
79F TYR* 5.9 2.0 - - - -
111F VAL* 5.1 1.6 - - - -
112F LEU* 1.3 78.5 - - - +
114F ARG* 1.3 68.6 + - - +
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Residues in contact with ARG 114 (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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7E PHE 3.7 8.9 + - - -
8E HIS* 3.4 70.1 + - + +
9E ARG* 5.4 5.5 + - + +
10E GLY 4.7 4.4 + - - -
12E PHE* 3.4 19.2 - - - -
75F HIS 4.0 4.3 - - - +
76F TRP* 3.3 43.0 - - + -
77F ASN* 4.3 1.8 - - - +
113F SER* 1.3 82.4 + - - +
115F LYS* 1.3 62.0 + - - +
116F ALA 5.1 1.1 - - - +
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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