Contacts of the strand formed by residues 118 - 127 (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 HIS 118 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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31E TRP* 3.6 5.9 - - - -
112E SER* 4.9 7.3 + - - -
113E THR* 2.6 32.3 + - - -
114E ASN* 3.1 41.8 + - + +
117E GLN* 1.3 107.8 + - - +
119E ALA* 1.3 58.9 + - - +
120E MET* 6.3 0.2 - - - +
137E LEU* 5.0 4.2 - - + +
138E TYR 3.2 10.5 - - - +
144E LEU* 4.3 8.3 - - + -
148E LEU* 3.6 39.5 - - + +
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Residues in contact with ALA 119 (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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27E PHE* 3.8 19.7 - - + -
31E TRP* 4.0 3.1 - - + -
110E VAL* 5.4 0.4 - - + -
112E SER 3.2 8.3 - - - +
113E THR* 3.4 17.5 - - - +
118E HIS* 1.3 79.6 - - - +
120E MET* 1.3 62.6 + - - +
121E VAL* 4.7 2.5 - - + -
136E THR 3.7 0.4 - - - +
137E LEU* 3.5 8.2 - - - +
138E TYR* 2.7 52.6 + - + -
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Residues in contact with MET 120 (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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110E VAL* 3.8 1.0 - - - +
111E VAL* 2.9 41.7 + - + -
112E SER* 2.8 30.3 + - - +
118E HIS* 6.3 0.4 - - - +
119E ALA* 1.3 77.0 - - - +
121E VAL* 1.3 66.8 + - - +
135E ILE* 4.6 4.7 - - + -
136E THR 3.2 5.8 - - - +
137E LEU* 3.8 15.7 - - + -
148E LEU 5.8 0.2 - - - +
151E ASN* 5.0 7.2 - - + +
152E PHE* 3.7 39.5 - - + -
155E PHE* 3.9 31.9 - - + -
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Residues in contact with VAL 121 (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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27E PHE* 4.2 14.4 - - + -
56E TYR* 4.9 2.5 - - - +
108E VAL* 3.6 22.0 - - + -
109E ARG 3.6 9.4 - - - +
110E VAL* 4.4 10.8 - - + -
111E VAL* 4.5 0.4 - - - -
119E ALA* 4.7 0.4 - - + -
120E MET* 1.3 81.0 - - - +
122E PHE* 1.3 62.9 + - - +
123E PHE* 3.4 34.0 - - + -
135E ILE* 3.3 6.8 - - - -
136E THR* 2.9 31.9 + - - +
138E TYR* 3.6 32.3 - - + -
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Residues in contact with PHE 122 (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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11E PRO* 4.0 14.8 - - + -
13E LEU* 3.9 22.7 - - + -
16E VAL* 3.6 44.6 - - + -
107E LEU* 5.0 4.3 - - + -
108E VAL* 3.4 3.5 - - - -
109E ARG* 2.8 48.1 + - + +
111E VAL* 3.8 6.0 - - + +
121E VAL* 1.3 74.4 - - - +
123E PHE* 1.3 64.5 + - - +
124E LYS* 3.7 32.5 - - + -
133E PHE* 3.9 32.1 - + + -
134E LYS 3.6 7.6 - - - -
135E ILE* 4.2 6.3 - - + +
155E PHE* 5.5 0.4 - - + -
159E LEU* 4.2 11.9 - - + -
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Residues in contact with PHE 123 (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* 4.3 2.9 - - - -
83E PHE* 4.1 11.9 - + - -
106E TYR* 3.8 18.6 - + + +
107E LEU 3.3 5.4 - - - +
108E VAL* 3.8 29.4 - - + -
121E VAL* 3.4 37.2 - - + -
122E PHE* 1.3 79.6 - - - +
124E LYS* 1.3 61.1 + - - +
133E PHE* 3.2 7.4 - - - +
134E LYS* 2.9 53.0 + - + +
136E THR* 3.6 16.6 - - - -
138E TYR* 3.9 9.9 - - - -
202E 4OL 3.8 18.2 - - + -
203E SO4 3.4 23.1 - - - -
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Residues in contact with LYS 124 (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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10E ALA* 4.2 13.7 - - + -
11E PRO 5.2 3.1 - - - +
13E LEU* 4.3 25.8 - - + -
105E SER* 4.5 5.5 + - - -
106E TYR* 3.3 3.2 - - - -
107E LEU* 2.7 52.2 + - + +
122E PHE* 3.7 20.9 - - + -
123E PHE* 1.3 75.8 - - - +
125E LYS* 1.3 65.7 + - - +
126E VAL* 4.6 10.9 - - - +
131E GLU* 3.1 32.3 + - + +
132E TYR 3.4 10.3 - - - +
133E PHE* 4.6 1.6 - - + -
202E 4OL 4.2 0.7 - - - -
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Residues in contact with LYS 125 (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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103E LEU* 4.0 10.9 - - + +
105E SER* 3.2 7.4 - - - +
106E TYR* 3.5 31.9 - - + -
124E LYS* 1.3 75.8 - - - +
126E VAL* 1.3 65.0 + - - +
127E SER* 3.8 22.3 + - - -
130E ARG 3.6 0.5 - - - +
131E GLU* 3.6 2.6 - - - +
132E TYR* 2.8 42.0 + - + +
202E 4OL 2.9 78.6 + - + +
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Residues in contact with VAL 126 (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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103E LEU* 3.5 4.6 - - - +
104E THR* 2.9 42.1 + - + -
105E SER* 2.9 30.8 + - - +
124E LYS* 4.6 6.3 - - - +
125E LYS* 1.3 76.5 - - - +
127E SER* 1.3 62.8 + - - +
129E ASN* 3.8 27.1 - - - +
130E ARG 3.3 8.5 - - - +
131E GLU* 4.1 24.9 - - + +
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Residues in contact with SER 127 (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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101E PRO 5.2 1.4 + - - -
102E GLY* 3.4 13.0 + - - -
103E LEU* 4.4 4.6 - - - +
125E LYS* 3.8 27.6 + - - -
126E VAL* 1.3 76.8 - - - +
128E GLN* 1.3 94.4 + - - +
129E ASN 3.1 0.2 - - - -
130E ARG* 2.9 26.6 + - - +
132E TYR* 4.2 10.0 - - - -
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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