Contacts of the strand formed by residues 100 - 108 (chain E) in PDB entry 4GG6
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 100 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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43E ARG* 4.6 4.7 - - + -
44E GLN 3.4 27.4 - - - +
45E LEU* 3.6 14.4 - - + +
46E PRO* 4.4 5.6 - - - -
98E ASP 3.3 4.9 + - - +
99E ALA* 1.3 76.3 - - - +
101E VAL* 1.3 64.6 + - - +
102E TYR* 3.3 19.7 - - + +
123E HIS* 4.9 2.2 - - - -
124E LEU 3.1 29.2 + - - -
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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
----------------------------------------------------------
42E TYR 3.7 0.3 - - - +
43E ARG* 3.0 6.8 - - - -
44E GLN* 2.8 39.4 + - + +
46E PRO* 5.9 3.1 - - + -
100E ALA* 1.3 75.1 - - - +
102E TYR* 1.3 63.6 + - - +
103E TYR* 3.9 26.2 + - + +
120E LYS 3.9 21.3 - - - +
121E GLY 4.2 0.4 - - - -
122E THR 3.2 17.0 - - - +
123E HIS* 3.5 35.9 - - + +
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Residues in contact with TYR 102 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6E GLN* 2.9 21.6 + - - -
21E LEU* 3.7 16.2 - - + -
41E TRP* 4.2 8.5 - + + -
42E TYR 3.3 6.7 - - - -
43E ARG* 3.5 40.4 + - + -
53E VAL* 4.5 4.9 - - + -
89E LEU* 3.6 27.6 - - + -
91E LEU* 4.0 16.8 - - + +
98E ASP* 2.8 32.7 + - - +
100E ALA* 3.3 26.3 - - + +
101E VAL* 1.3 72.8 - - - +
103E TYR* 1.3 61.2 + - - +
122E THR* 2.8 31.7 + - - +
124E LEU* 3.7 22.4 - - + -
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Residues in contact with TYR 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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6E GLN* 4.0 2.9 - - - -
40E HIS 3.6 0.9 - - - +
41E TRP* 3.3 10.7 - - - -
42E TYR* 2.8 46.5 + - + +
43E ARG 4.8 0.2 - - - -
44E GLN* 2.6 42.6 + - + -
50E PRO* 4.9 1.3 - - + -
101E VAL* 3.9 18.3 - - + +
102E TYR* 1.3 72.6 - - - +
104E CYS* 1.3 60.3 + - - +
105E ILE* 4.1 6.0 - - + +
118E PHE* 3.7 38.1 - + + -
119E GLY 3.7 17.5 - - - -
120E LYS 3.4 19.3 - - - -
121E GLY* 3.6 16.8 - - - -
44F GLN* 3.1 13.5 + - - -
49F GLY* 5.7 1.2 - - - -
50F LEU* 4.2 12.7 + - + -
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Residues in contact with CYS 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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4E THR* 2.7 29.7 + - - -
6E GLN* 3.1 26.1 + - - +
23E CYS* 2.0 50.5 - - + -
25E HIS* 4.3 5.8 - - - -
39E ILE* 4.3 5.6 - - - -
40E HIS 3.4 2.9 - - - -
41E TRP* 3.7 20.6 - - + -
87E SER* 4.2 3.8 - - - -
103E TYR* 1.3 72.6 - - - +
105E ILE* 1.3 67.3 + - - +
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Residues in contact with ILE 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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4E THR* 4.5 1.6 - - - +
38E TYR 3.6 0.7 - - - +
39E ILE* 3.5 5.2 - - - +
40E HIS* 2.8 50.1 + - + +
103E TYR* 4.2 6.7 - - + +
104E CYS* 1.3 88.9 - - - +
106E LEU* 1.3 71.4 + - - +
107E ARG* 3.7 14.1 - - + +
115E GLY* 3.3 27.6 - - - +
117E THR 4.0 6.3 - - - +
118E PHE* 3.6 53.4 - - + -
119E GLY 4.1 7.4 - - - +
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Residues in contact with LEU 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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3E LYS 4.9 8.5 - - - +
4E THR* 3.8 17.4 - - + +
25E HIS* 3.8 29.6 - - + -
27E THR* 5.0 3.1 - - - +
28E ILE* 3.7 48.9 - - + +
37E ASP* 4.4 13.7 - - + +
38E TYR 3.4 9.4 - - - +
39E ILE* 3.8 11.9 - - + -
105E ILE* 1.3 79.9 - - - +
107E ARG* 1.3 65.2 + - - +
114E ASP 4.9 0.7 - - - +
115E GLY* 3.7 13.2 - - - -
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Residues in contact with ARG 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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37E ASP* 3.3 5.4 - - - -
38E TYR* 2.6 39.9 + - - +
40E HIS* 3.7 28.0 + - + +
42E TYR* 4.1 14.1 + - - -
105E ILE* 3.7 11.3 + - + +
106E LEU* 1.3 74.5 - - - +
108E ASP* 1.3 60.4 + - - +
111E GLY* 5.8 1.8 - - - -
114E ASP 5.5 0.2 - - - -
115E GLY* 2.8 31.6 + - - +
116E LEU* 3.2 33.7 + - - +
118E PHE* 3.5 16.5 - - - -
42F TYR* 3.6 2.6 + - - -
112F GLY* 3.1 44.0 + - - +
114F TYR 4.8 0.2 + - - -
116F GLN* 2.9 31.0 + - - -
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Residues in contact with ASP 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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58C PHE* 4.2 10.8 - - + -
29E SER* 5.0 0.7 + - - -
36E THR* 3.4 23.8 - - - +
37E ASP* 3.5 11.2 + - - +
107E ARG* 1.3 72.4 - - - +
109E GLY* 1.3 57.2 + - - +
110E ARG* 2.9 59.6 + - - +
111E GLY* 2.6 41.4 + - - +
114E ASP 5.5 4.1 + - - +
112F GLY* 3.3 10.5 - - - -
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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