Contacts of the strand formed by residues 97 - 114 (chain E) 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 ALA 97 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39E LEU* 5.3 2.2 - - + -
90E LEU* 4.6 14.4 - - + -
91E THR 3.4 7.9 - - - +
92E MET* 3.5 21.1 - - + -
96E GLN* 1.3 73.7 - - - +
98E ALA* 1.3 63.5 + - - +
45F ASN* 6.0 2.5 - - - +
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Residues in contact with ALA 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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90E LEU* 4.2 8.1 - - - +
91E THR* 2.8 48.5 + - - +
93E ASP* 5.1 1.1 - - + -
96E GLN* 3.5 6.5 + - + +
97E ALA* 1.3 76.9 - - - +
99E TRP* 1.3 59.1 + - - +
100E ARG* 3.2 32.7 + - + +
49F PHE* 6.3 0.4 - - + -
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Residues in contact with TRP 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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42E VAL* 4.5 15.5 - - + -
51E GLN* 4.2 4.5 - - - -
88E LYS* 3.0 55.0 + - + +
89E ALA* 3.3 9.4 - - - -
90E LEU* 2.9 49.5 - - + +
98E ALA* 1.3 70.8 - - - +
100E ARG* 1.3 68.3 + - - +
42F VAL* 4.8 4.6 - - - +
44F ILE* 3.4 50.0 - - + +
49F PHE* 3.4 35.4 - + + -
99F TRP* 3.5 35.5 - + - -
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Residues in contact with ARG 100 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30E ASP* 5.2 11.9 - - + -
32E LYS* 3.9 27.4 - - - +
36E VAL* 6.0 2.5 - - + -
88E LYS* 3.5 9.7 - - - +
89E ALA* 2.8 36.3 + - - +
91E THR* 2.8 28.5 - - + +
93E ASP* 4.0 27.7 + - - +
98E ALA* 3.2 26.2 - - - +
99E TRP* 1.3 79.8 + - - +
101E PHE* 1.3 64.9 + - - +
102E ILE* 3.5 4.1 + - + +
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Residues in contact with PHE 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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30E ASP* 3.5 5.4 - - - +
31E ILE* 3.3 37.1 + - + +
86E PHE* 4.2 15.6 - - + -
87E VAL* 3.3 8.1 - - - -
88E LYS* 3.3 56.3 - - + -
100E ARG* 1.3 72.2 - - - +
102E ILE* 1.3 60.4 + - - +
21F TRP* 3.7 40.6 - + + -
52F TYR* 3.9 32.8 - + + -
53F PHE* 5.2 0.4 - + - -
54F PHE 5.2 1.1 - - - -
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Residues in contact with ILE 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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25E LYS* 4.3 5.2 - - + -
28E ALA* 3.9 21.1 - - + -
29E THR 3.5 6.5 - - - +
30E ASP* 4.6 2.0 - - + -
36E VAL* 4.1 17.9 - - + -
38E VAL* 4.3 5.2 - - + -
53E PHE* 3.6 25.8 - - + -
86E PHE* 3.5 5.8 - - - -
87E VAL 2.7 42.2 + - - +
89E ALA* 3.5 21.3 - - + -
91E THR* 3.7 26.0 - - + -
100E ARG* 4.1 2.9 - - + +
101E PHE* 1.3 77.2 - - - +
103E ARG* 1.3 59.5 + - - +
104E ILE* 3.3 15.2 - - + +
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Residues in contact with ARG 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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327B PHE* 3.4 52.6 - - - +
349B ASN* 2.7 39.8 + - - -
350B GLN* 3.7 15.7 + - - -
25E LYS* 5.5 1.9 + - - -
28E ALA* 4.5 10.7 - - - +
29E THR* 3.0 24.6 + - - +
30E ASP 5.9 0.4 + - - -
84E HIS* 2.7 59.9 + - + -
85E THR 3.6 4.0 - - - +
86E PHE* 3.4 31.0 - - + -
102E ILE* 1.3 72.4 - - - +
104E ILE* 1.3 63.6 + - - +
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Residues in contact with ILE 104 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25E LYS* 4.1 15.7 - - + +
53E PHE* 4.8 9.2 - - + -
54E PHE 4.9 6.7 - - - +
55E GLU* 2.8 27.8 - - - +
84E HIS* 3.3 6.4 - - - +
85E THR* 2.9 51.8 + - + +
87E VAL* 3.4 30.5 - - + -
102E ILE* 3.3 28.5 - - + +
103E ARG* 1.3 79.7 - - - +
105E ASP* 1.3 69.4 + - - +
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Residues in contact with ASP 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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54E PHE 4.0 1.6 - - - +
55E GLU* 3.5 26.8 + - + +
56E THR 3.3 29.4 + - - +
57E LYS* 3.8 23.2 + - + +
82E THR* 3.8 14.3 - - + +
83E THR 3.9 5.8 - - - -
84E HIS* 3.3 20.2 + - - -
104E ILE* 1.3 81.1 - - - +
106E THR* 1.3 59.7 + - - +
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Residues in contact with THR 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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350A GLN* 6.0 0.2 + - - -
54E PHE 5.5 0.2 - - - -
56E THR* 3.1 22.7 + - - +
83E THR* 3.1 14.4 + - - +
84E HIS 3.3 27.1 - - - +
85E THR* 3.3 18.8 - - - +
104E ILE 3.4 0.2 + - - -
105E ASP* 1.3 74.6 - - - +
107E ALA* 1.3 68.1 + - + +
84F HIS 4.7 2.8 - - - +
85F THR* 3.5 11.9 + - - -
106F THR* 2.5 50.1 + - - +
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Residues in contact with ALA 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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56E THR* 3.0 16.5 + - - +
82E THR* 3.3 13.5 - - - +
83E THR* 3.2 30.6 + - - +
106E THR* 1.3 82.7 - - + +
108E CYS* 1.3 63.8 + - - +
109E VAL* 4.8 3.1 - - + -
83F THR* 4.8 4.3 - - - +
107F ALA* 3.7 29.4 - - + -
109F VAL* 5.2 3.8 - - + -
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Residues in contact with CYS 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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14E VAL* 5.9 0.2 - - - +
15E CYS* 3.7 30.3 - - + +
16E ASP 3.8 6.7 - - - -
17E SER* 3.7 26.2 - - - -
58E CYS* 2.0 51.4 - - - +
80E CYS* 3.9 7.0 - - - -
81E THR 3.5 3.6 - - - -
107E ALA* 1.3 77.7 - - - +
109E VAL* 1.3 63.6 + - - +
109F VAL* 4.5 9.9 - - - +
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Residues in contact with VAL 109 (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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297B HIS* 4.4 10.8 - - + +
14E VAL* 5.9 0.9 - - - -
15E CYS* 3.6 6.3 - - - -
80E CYS* 3.2 2.1 - - - -
81E THR* 2.8 50.3 + - + +
83E THR* 3.2 37.0 - - + +
107E ALA* 4.8 3.6 - - + -
108E CYS* 1.3 79.5 - - - +
110E CYS* 1.3 66.7 + - - +
14F VAL* 5.4 4.7 - - + -
107F ALA* 5.1 3.8 - - + -
108F CYS 4.5 15.9 - - - +
109F VAL* 4.5 11.2 - - + -
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Residues in contact with CYS 110 (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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297B HIS* 5.6 0.9 + - - -
14E VAL* 3.9 11.3 - - + +
15E CYS* 3.6 9.3 - - - -
68E CYS* 2.0 48.7 - - + -
71E ILE* 4.0 8.7 - - - -
78E SER* 4.0 7.9 - - - -
79E TYR 3.4 3.8 - - - -
109E VAL* 1.3 78.4 - - - +
111E VAL* 1.3 62.6 + - - +
112E LEU* 4.0 15.5 - - - -
12F PHE 4.4 0.3 - - - +
13F SER* 4.5 2.1 - - - -
14F VAL* 3.5 37.1 + - + +
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Residues in contact with VAL 111 (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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297B HIS* 3.9 22.0 - - + +
78E SER* 3.1 25.8 - - - -
79E TYR* 2.7 53.6 + - + +
81E THR* 3.4 32.8 - - + -
109E VAL* 4.8 0.4 - - + -
110E CYS* 1.3 73.9 - - - +
112E LEU* 1.3 64.7 + - - +
113E SER* 5.3 0.2 - - - -
11F GLU* 3.8 25.8 - - + +
12F PHE 3.8 6.3 - - - +
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Residues in contact with LEU 112 (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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71E ILE* 5.2 5.2 - - + -
76E TRP* 3.9 23.6 - - + -
77E ASN 3.7 7.0 - - - +
78E SER* 5.2 1.3 - - - -
110E CYS* 3.9 13.5 - - - +
111E VAL* 1.3 77.3 - - - +
113E SER* 1.3 62.1 + - - +
10F GLY 3.8 0.4 - - - +
11F GLU* 3.2 9.4 - - - +
12F PHE* 2.9 36.3 + - + +
14F VAL* 3.6 36.8 - - + +
69F ARG* 3.2 47.1 - - + +
70F GLY* 3.6 11.9 - - - +
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Residues in contact with SER 113 (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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76E TRP* 3.6 3.9 - - - -
77E ASN* 2.7 52.5 + - - +
79E TYR* 6.0 2.0 - - - -
111E VAL* 5.3 1.1 - - - -
112E LEU* 1.3 76.2 - - - +
114E ARG* 1.3 67.2 + - - +
9F ARG 4.8 6.4 + - - -
10F GLY 4.1 8.3 + - - -
11F GLU* 4.6 17.8 - - - +
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Residues in contact with ARG 114 (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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75E HIS* 3.6 12.1 - - + +
76E TRP* 3.6 38.3 - - + -
77E ASN* 4.6 4.9 + - - -
113E SER* 1.3 83.3 + - - +
115E LYS* 1.3 64.0 + - - +
7F PHE 4.4 4.6 + - - -
8F HIS* 3.5 65.8 + - + +
9F ARG* 5.4 4.1 + - - -
10F GLY 4.7 4.2 + - - -
12F PHE* 4.3 10.9 - - - -
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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