Contacts of the strand formed by residues 128 - 138 (chain E) in PDB entry 5IXM
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 TYR 128 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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114E PHE* 5.4 0.7 - - - -
126E ASP* 3.5 15.2 - - - +
127E GLY* 1.3 81.7 - - - +
129E ALA* 1.3 73.2 + - - +
130E THR* 3.7 17.0 - - - -
151E PHE* 4.1 7.0 - + + -
152E GLN 3.2 16.6 - - - +
153E VAL* 3.7 14.4 - - + +
154E PHE* 3.5 15.4 - - - -
108F ASP* 3.1 34.7 + - - -
109F ASN 4.2 2.7 - - - -
110F PRO* 3.4 34.8 - - + -
113F ALA* 3.9 24.0 + - + -
116F LYS* 4.5 12.6 - - - +
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Residues in contact with ALA 129 (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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106E THR* 3.4 37.2 - - + +
107E ARG* 5.0 0.2 - - - -
108E VAL* 5.4 0.9 - - + -
114E PHE* 5.2 2.0 - - + -
128E TYR* 1.3 77.0 - - - +
130E THR* 1.3 63.3 + - - +
131E GLN* 4.5 0.3 - - - +
151E PHE* 3.4 9.0 - - - +
152E GLN* 2.9 45.9 + - + +
154E PHE* 4.2 10.3 - - + -
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Residues in contact with THR 130 (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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104E ASN* 3.0 33.7 + - - +
105E TYR 3.5 0.3 - - - -
106E THR* 2.9 27.2 + - - -
128E TYR* 3.7 20.5 + - - -
129E ALA* 1.3 72.7 - - - +
131E GLN* 1.3 63.9 + - - +
132E ILE* 3.8 28.7 - - + -
151E PHE* 3.9 13.3 - - + -
117F GLU* 4.9 4.2 + - - +
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Residues in contact with GLN 131 (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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104E ASN 3.4 2.2 - - - -
105E TYR* 3.4 35.8 + - + -
106E THR 2.9 29.6 + - - +
107E ARG* 3.7 20.4 - - - +
129E ALA 4.5 0.7 - - - +
130E THR* 1.3 74.7 - - - +
132E ILE* 1.3 60.2 + - - +
133E PHE* 4.9 4.0 - - + -
148E SER* 3.6 2.9 + - - +
150E GLN* 2.8 77.2 + - + +
151E PHE 4.4 1.0 + - - -
152E GLN* 3.7 24.0 + - - +
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Residues in contact with ILE 132 (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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102E ASN 5.2 1.1 - - - +
103E ILE* 3.5 3.3 - - - +
104E ASN* 2.9 48.8 + - + +
105E TYR* 4.5 0.6 - - - +
130E THR* 3.8 20.0 - - + -
131E GLN* 1.3 77.7 - - - +
133E PHE* 1.3 69.2 + - - +
134E THR* 3.9 19.1 - - - +
148E SER 3.2 5.6 - - - +
149E LYS* 3.8 28.9 - - + -
150E GLN 4.5 2.0 - - - +
151E PHE* 4.6 3.6 - - + -
117F GLU* 3.6 38.8 - - + +
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Residues in contact with PHE 133 (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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89E TRP* 4.1 15.5 - + - -
102E ASN 3.8 2.5 - - - -
103E ILE* 3.6 41.7 - - + -
105E TYR* 3.7 40.6 - + + -
131E GLN* 4.9 2.7 - - + -
132E ILE* 1.3 77.4 - - - +
134E THR* 1.3 67.3 + - - +
146E LEU 4.6 0.2 - - - -
147E SER* 3.1 3.2 - - - -
148E SER* 2.9 48.5 + - - +
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Residues in contact with THR 134 (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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100E ARG* 5.1 2.9 - - + +
101E PHE* 3.5 3.3 - - - +
102E ASN* 2.9 62.7 + - + +
103E ILE* 5.0 1.5 - - - +
132E ILE* 3.9 11.7 - - - +
133E PHE* 1.3 74.2 + - - +
135E ALA* 1.3 64.6 + - - +
136E GLY 5.1 0.2 - - - +
145E THR* 3.7 23.6 - - + -
146E LEU 3.5 4.0 - - - -
147E SER* 2.9 15.8 + - - -
149E LYS* 5.4 1.2 - - - -
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Residues in contact with ALA 135 (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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100E ARG 3.2 5.6 - - - -
101E PHE* 3.7 25.8 - - + -
134E THR* 1.3 75.0 - - - +
136E GLY* 1.3 57.7 + - - +
145E THR* 4.6 3.1 - - - -
146E LEU* 2.9 37.6 + - + +
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Residues in contact with GLY 136 (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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98E VAL 3.6 0.3 - - - +
99E TRP* 3.6 11.3 - - - -
100E ARG* 2.9 41.5 + - - +
101E PHE* 5.2 1.1 - - - -
134E THR* 5.1 0.6 - - - +
135E ALA* 1.3 75.8 - - - +
137E TYR* 1.3 60.7 + - - -
144E ALA 3.2 13.9 - - - -
145E THR* 4.0 7.4 - - - +
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Residues in contact with TYR 137 (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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98E VAL* 3.2 46.8 - - + +
99E TRP* 4.0 33.7 - + + -
100E ARG* 5.1 0.7 - - - -
136E GLY* 1.3 74.1 - - - -
138E ALA* 1.3 76.6 + - - +
139E ASN* 3.5 33.7 + - - +
142E TRP* 3.9 29.4 - + + -
143E ASN* 3.3 1.6 - - - +
144E ALA* 2.9 35.7 + - + +
145E THR* 5.0 0.5 + - - -
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Residues in contact with ALA 138 (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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98E VAL* 2.9 36.1 + - - +
100E ARG* 4.0 22.2 - - + +
137E TYR* 1.3 82.6 - - - +
139E ASN* 1.3 60.6 + - - +
142E TRP 3.6 6.1 - - - -
143E ASN* 3.6 14.1 - - + -
25F TYR* 3.5 26.5 - - + +
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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