Contacts of the strand formed by residues 120 - 128 (chain E) in PDB entry 1LVO
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 CYS 120 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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28E ASN* 4.1 0.6 + - - -
70E ASN* 5.7 7.9 - - - +
116E CYS* 4.0 3.1 - - - -
117E TYR* 3.0 34.6 + - + +
118E GLU 4.8 1.6 - - - +
119E GLY* 1.3 80.0 - - - +
121E PRO* 1.4 79.2 - - - +
122E GLY* 3.2 2.4 + - - -
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Residues in contact with PRO 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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14E GLU* 4.1 23.3 - - + +
17E ILE* 3.9 29.6 - - + -
69E LYS* 4.7 5.8 - - - +
114E LEU* 4.1 12.3 - - + -
116E CYS* 3.8 11.2 - - - -
119E GLY 3.7 7.4 - - - +
120E CYS* 1.4 92.3 - - + +
122E GLY* 1.3 59.2 + - - +
9F PRO* 3.6 24.5 - - + +
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Residues in contact with GLY 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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115E ALA 2.8 16.8 + - - -
116E CYS* 5.0 0.4 - - - -
120E CYS* 3.2 5.3 + - - -
121E PRO* 1.3 73.9 - - - +
123E SER* 1.3 61.9 + - - +
2002E DIO 4.0 24.5 - - - +
8F GLN* 4.0 9.7 - - - +
9F PRO* 3.4 15.1 - - - +
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Residues in contact with SER 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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114E LEU* 3.5 8.1 - - - +
115E ALA* 2.8 45.8 + - - +
121E PRO 4.0 0.2 - - - -
122E GLY* 1.3 80.4 - - - +
124E VAL* 1.3 61.9 + - - +
125E TYR* 3.8 2.3 - - - -
2002E DIO 3.6 9.3 - - - -
6F MET* 3.4 36.4 - - - -
7F ALA 3.0 13.2 - - - -
9F PRO* 4.1 3.7 - - - +
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Residues in contact with VAL 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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7E ALA* 3.6 16.2 - - + +
8E GLN 4.0 2.2 - - - +
10E SER* 4.3 11.9 - - - +
112E ASN* 4.9 0.4 - - + -
113E ILE 3.3 13.5 - - - +
114E LEU* 4.3 9.0 - - + -
123E SER* 1.3 76.2 - - - +
125E TYR* 1.3 67.4 + - - +
149E TYR* 3.3 27.6 - - + +
6F MET* 4.0 0.3 - - - -
7F ALA* 2.7 44.3 + - + +
8F GLN 4.3 8.1 - - - +
9F PRO* 5.2 0.4 - - + -
124F VAL* 3.4 28.8 - - + +
125F TYR* 5.7 0.5 - - - -
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Residues in contact with TYR 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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6E MET 5.4 0.2 - - - -
7E ALA* 3.6 9.2 - - - +
112E ASN* 3.7 1.7 - - - -
113E ILE* 3.0 41.3 + - + +
115E ALA* 3.7 20.5 - - + +
123E SER* 3.8 4.9 - - - -
124E VAL* 1.3 81.4 - - - +
126E GLY* 1.3 63.2 + - - +
127E VAL* 3.7 26.2 - - + -
137E GLY* 4.2 3.4 - - - -
138E SER 3.1 36.8 + - - -
139E PHE* 3.5 20.1 - - - -
4F ARG* 4.0 17.7 - - - +
5F LYS 4.2 17.5 - - - +
6F MET* 3.2 32.8 - - + -
124F VAL 5.8 0.2 - - - -
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Residues in contact with GLY 126 (chain E).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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5E LYS* 3.6 27.2 - - - +
6E MET 3.5 26.1 + - - -
7E ALA* 3.8 3.3 - - - +
111E PHE 3.4 9.4 - - - -
112E ASN* 4.7 0.2 - - - -
125E TYR* 1.3 79.1 - - - +
127E VAL* 1.3 64.8 + - - +
286E GLU* 5.4 0.3 - - - +
4F ARG* 4.3 8.7 + - - -
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Residues in contact with VAL 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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5E LYS* 3.6 9.2 + - - +
110E SER* 3.3 4.5 - - - -
111E PHE* 2.8 69.9 + - + +
113E ILE* 3.8 14.4 - - + -
125E TYR* 3.7 27.6 - - + -
126E GLY* 1.3 79.7 - - - +
128E ASN* 1.3 63.1 + - - +
135E ILE* 4.1 17.9 - - + -
136E LYS 4.4 14.8 - - - +
137E GLY* 4.6 0.7 - - - -
286E GLU* 4.6 4.7 - - - -
4F ARG* 4.6 2.2 - - - +
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Residues in contact with ASN 128 (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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108E GLY* 3.0 38.5 + - - -
109E GLU 3.2 11.2 - - - -
110E SER* 2.7 22.8 + - - +
111E PHE* 4.8 0.7 - - - +
127E VAL* 1.3 77.6 - - - +
129E MET* 1.3 67.8 + - - +
130E ARG* 3.6 9.5 + - - +
135E ILE* 3.8 13.2 - - - +
136E LYS 5.0 1.6 + - - -
202E ASN* 3.5 12.3 + - - +
285E ASP* 3.5 8.4 - - - +
286E GLU* 3.5 38.7 + - - +
288E THR* 4.0 2.2 - - - +
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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