Contacts of the strand formed by residues 112 - 117 (chain E) in PDB entry 5LS6
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 VAL 112 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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67D PRO* 4.8 5.4 - - + -
68D VAL* 3.3 46.0 - - + +
101E PHE* 3.1 8.2 - - - -
102E ASN* 2.8 43.0 + - + +
105E SER* 4.7 9.8 + - - +
110E PRO 3.4 13.9 + - - +
111E LEU* 1.3 73.3 - - - +
113E PHE* 1.3 58.6 + - - +
123E LEU* 5.1 5.4 - - + -
124E TYR 3.2 20.9 - - - +
125E GLU* 4.5 1.3 - - - +
135E LEU* 4.1 10.3 - - + -
152E TRP* 5.0 11.2 - - + -
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Residues in contact with PHE 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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99E VAL* 3.9 9.2 - - + -
100E GLN 3.2 15.0 - - - +
101E PHE* 3.6 33.2 - + + -
102E ASN 4.5 0.4 - - - +
111E LEU 4.8 0.2 - - - -
112E VAL* 1.3 74.1 - - - +
114E ALA* 1.3 67.0 + - - +
115E THR* 3.8 11.7 - - + -
123E LEU* 3.5 3.5 - - - +
124E TYR* 2.7 78.1 + + + +
126E CYS* 3.6 16.8 - - - -
132E ILE* 4.0 11.2 - - + -
152E TRP* 4.4 5.6 - - - +
426E ILE* 3.3 39.0 - - + -
434E ILE* 4.2 9.4 - - + -
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Residues in contact with ALA 114 (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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99E VAL* 3.2 12.2 - - - +
100E GLN 3.0 29.6 + - - +
113E PHE* 1.3 73.0 - - - +
115E THR* 1.3 65.3 + - - +
121E VAL* 4.4 1.6 - - + -
122E THR 3.2 10.8 - - - +
123E LEU* 4.6 3.6 - - + -
150E CYS* 4.3 10.1 - - - -
152E TRP* 3.9 14.3 - - + +
163E LEU* 3.8 28.9 - - + -
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Residues in contact with THR 115 (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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90E GLU* 2.7 26.0 + - - +
96E LEU* 4.4 11.4 - - - -
98E GLY 3.4 9.2 - - - -
99E VAL* 4.1 8.3 - - + -
113E PHE* 3.8 16.2 - - + -
114E ALA* 1.3 81.5 - - - +
116E VAL* 1.3 63.4 + - - +
120E ARG* 3.8 1.7 - - - +
121E VAL* 3.6 1.4 - - - -
122E THR* 2.7 34.7 + - - -
124E TYR* 3.5 25.9 - - + -
428E VAL* 4.2 4.7 - - + -
434E ILE* 3.8 9.6 - - + -
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Residues in contact with VAL 116 (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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96E LEU* 3.2 9.9 - - - -
97E PHE 3.2 21.9 + - - -
98E GLY* 3.1 30.0 + - - +
115E THR* 1.3 72.9 - - - +
117E GLY* 1.3 60.0 + - - +
120E ARG 3.5 2.5 - - - -
121E VAL* 3.7 30.5 - - + -
147E PHE* 3.9 21.3 - - + -
148E TYR 4.0 1.1 - - - -
149E THR* 3.7 26.5 - - - +
150E CYS* 3.9 18.8 - - + +
165E VAL* 3.9 7.4 - - + -
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Residues in contact with GLY 117 (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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92E HIS* 4.5 4.7 - - - -
95E PRO 3.1 17.5 - - - -
96E LEU* 4.1 6.9 - - - +
97E PHE* 4.5 1.1 - - - -
116E VAL* 1.3 76.9 - - - +
118E SER* 1.3 77.5 + - - +
120E ARG* 2.8 25.2 + - - +
147E PHE* 4.2 8.3 + - - +
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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