Contacts of the strand formed by residues 103 - 113 (chain E) in PDB entry 4ZHF
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 LEU 103 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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94E LEU* 3.7 30.7 - - + -
97E ILE* 3.9 26.3 - - + +
98E LYS* 5.5 3.5 - - - +
100E TYR* 3.2 35.8 + - + +
101E PRO 3.2 2.3 + - - +
102E GLY* 1.3 76.2 - - - +
104E THR* 1.3 60.1 + - - +
105E SER 3.6 16.2 - - - +
106E TYR* 4.4 6.1 - - + -
125E LYS* 4.0 29.8 - - + +
126E VAL 3.5 17.0 - - - +
127E SER* 4.4 2.5 - - - +
202E 4OL 4.9 6.3 - - + -
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Residues in contact with THR 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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97E ILE* 4.1 8.9 - - - +
102E GLY 3.6 6.2 + - - -
103E LEU* 1.3 75.1 + - - +
105E SER* 1.3 67.4 + - - +
126E VAL* 2.9 28.5 + - + -
127E SER* 5.4 0.2 - - - -
128E GLN 5.5 0.9 + - - -
129E ASN* 5.5 7.5 + - - +
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Residues in contact with SER 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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97E ILE* 4.0 7.6 - - - +
103E LEU* 3.6 5.6 - - - +
104E THR* 1.3 86.7 - - - +
106E TYR* 1.3 62.9 + - - +
124E LYS* 4.5 7.0 + - - -
125E LYS* 3.2 5.6 - - - +
126E VAL* 2.9 51.4 + - - +
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Residues in contact with TYR 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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79E TRP* 4.5 7.3 - + - -
81E ARG* 5.8 0.7 + - - -
83E PHE* 4.5 5.6 - + - -
93E THR* 2.9 25.8 + - - -
94E LEU* 3.8 49.6 - - + -
97E ILE* 3.9 11.0 - - + +
103E LEU* 4.4 5.8 - - + -
105E SER* 1.3 77.5 - - - +
107E LEU* 1.3 65.8 + - - +
108E VAL* 3.7 27.4 - - + -
123E PHE* 3.8 17.4 - + + -
124E LYS 3.3 3.8 - - - -
125E LYS* 3.5 26.9 - - + -
202E 4OL 3.0 51.7 + + - -
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Residues in contact with LEU 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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13E LEU* 4.0 37.7 - - + -
91E GLU* 4.8 16.2 - - + +
92E PHE 3.7 11.0 - - - +
93E THR* 5.8 1.3 - - - -
106E TYR* 1.3 78.0 - - - +
108E VAL* 1.3 78.2 + - - +
109E ARG* 4.8 12.6 - - + +
122E PHE* 3.8 6.9 - - + +
123E PHE* 3.3 5.0 - - - +
124E LYS* 2.7 51.0 + - + +
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Residues in contact with VAL 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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56E TYR* 5.4 0.9 - - + +
83E PHE* 3.9 27.4 - - + -
91E GLU* 3.2 7.2 - - - +
92E PHE* 2.9 58.0 + - + +
93E THR* 5.2 0.4 - - - -
106E TYR* 3.7 26.0 - - + -
107E LEU* 1.3 78.7 - - - +
109E ARG* 1.3 64.8 - - - +
110E VAL* 4.9 1.3 - - + +
121E VAL* 3.6 24.7 - - + -
122E PHE 3.4 3.4 - - - -
123E PHE* 3.8 15.0 - - + -
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Residues in contact with ARG 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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13E LEU* 3.1 43.9 + - - +
16E VAL* 2.7 38.9 + - + +
17E PRO 3.4 24.9 - - - +
18E LEU* 3.7 22.4 - - + +
88E GLN* 5.0 6.0 - - - +
90E GLY 3.6 3.1 - - - -
91E GLU* 2.6 30.5 + - + +
107E LEU* 4.8 7.5 - - + +
108E VAL* 1.3 76.5 - - - +
110E VAL* 1.3 64.9 + - - +
111E VAL 3.3 1.4 + - - -
121E VAL* 4.1 2.0 - - - -
122E PHE* 2.8 51.2 + - + +
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Residues in contact with VAL 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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18E LEU* 3.7 8.5 - - - +
19E GLN* 2.9 33.9 + - + +
22E PHE* 3.9 34.8 - - + -
27E PHE* 4.4 21.1 - - + -
90E GLY* 2.9 23.2 + - - +
92E PHE* 4.2 11.7 - - + -
108E VAL* 5.2 1.3 - - + -
109E ARG* 1.3 69.7 - - - +
111E VAL* 1.3 60.6 + - - +
112E SER 4.2 5.2 - - - +
113E THR* 4.3 12.3 - - + -
120E MET 4.0 8.7 - - - +
121E VAL* 4.4 12.1 - - + -
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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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16E VAL* 3.8 17.9 - - + -
17E PRO* 3.3 36.8 - - + +
18E LEU 3.7 2.4 - - - -
19E GLN* 3.1 18.0 + - - -
109E ARG 3.8 11.7 - - - +
110E VAL* 1.3 73.2 - - - +
112E SER* 1.3 65.9 + - - +
120E MET* 2.9 34.7 + - + +
121E VAL 4.5 0.7 - - - -
122E PHE* 3.8 11.4 - - + +
155E PHE* 4.0 26.9 - - + -
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Residues in contact with SER 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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19E GLN* 3.1 12.8 - - - -
110E VAL* 3.7 1.7 - - - +
111E VAL* 1.3 86.6 - - - +
113E THR* 1.3 64.1 + - - +
118E HIS* 4.9 8.2 + - - -
119E ALA* 3.2 1.0 - - - +
120E MET* 2.8 48.2 + - - +
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Residues in contact with THR 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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19E GLN* 2.8 28.7 + - + +
22E PHE* 4.9 0.2 - - + -
27E PHE* 4.1 10.6 - - + -
31E TRP* 3.8 3.1 - - - -
110E VAL* 4.3 6.7 - - + -
112E SER* 1.3 78.1 - - - +
114E ASN* 1.3 57.6 + - - +
115E TYR* 2.9 53.4 + - + -
118E HIS* 2.6 28.2 + - - -
119E ALA* 3.4 13.7 - - - +
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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