Contacts of the strand formed by residues 144 - 148 (chain C) in PDB entry 5L5E
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 LYS 144 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35C LYS* 4.2 2.0 - - - +
40C VAL* 3.8 5.4 - - - +
104C VAL* 3.8 27.8 - - + -
105C GLU* 5.9 1.6 - - + +
133C ILE 4.6 0.4 - - - -
134C ALA* 3.3 6.6 - - - +
135C GLY 3.1 39.6 + - - +
137C ASP* 4.1 20.6 + - - +
140C ASP* 3.9 15.3 + - - -
142C GLU* 3.7 38.1 + - - +
143C PRO* 1.3 79.4 - - - +
145C LEU* 1.3 62.3 + - - +
146C TYR* 4.4 17.4 + - + +
156C SER* 5.7 0.9 - - - +
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Residues in contact with LEU 145 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33C GLY* 3.4 33.2 - - - +
34C VAL* 4.1 3.1 - - - +
35C LYS* 4.0 14.1 - - + +
40C VAL* 4.4 5.8 - - + -
42C LEU* 4.2 16.2 - - + -
132C LEU* 4.6 9.6 - - + -
133C ILE 3.6 5.2 - - - +
134C ALA* 4.0 19.1 - - + -
144C LYS* 1.3 74.0 - - - +
146C TYR* 1.3 73.1 + - - +
156C SER* 3.2 10.0 + - - -
157C TRP* 2.9 50.3 + - + +
158C SER 4.1 4.3 - - - +
159C ALA* 4.1 10.3 - - - -
160C GLN* 4.3 4.3 - - + +
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Residues in contact with TYR 146 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104C VAL* 3.9 20.6 - - + -
105C GLU* 3.1 45.9 - - + +
108C THR* 3.4 35.4 - - + +
132C LEU* 3.4 9.1 - - - +
133C ILE* 2.8 34.7 + - + +
144C LYS* 4.4 20.7 + - + +
145C LEU* 1.3 77.5 - - - +
147C GLN* 1.3 59.2 + - - +
154C TYR* 4.2 11.0 - + - -
155C SER* 3.4 18.8 - - - -
156C SER* 3.7 26.9 + - - -
157C TRP* 4.7 2.5 - - - +
55D SER* 4.9 6.0 - - - -
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Residues in contact with GLN 147 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130C SER* 4.3 1.7 + - - -
131C THR 3.3 12.3 - - - +
132C LEU* 3.8 16.4 - - + -
146C TYR* 1.3 74.3 - - - +
148C THR* 1.3 81.2 + - - +
149C GLU* 4.2 18.0 + - - +
154C TYR* 3.2 26.9 - - - +
155C SER* 3.0 11.2 + - - +
157C TRP* 3.6 26.9 - - + +
160C GLN* 2.6 29.9 + - + -
162C ILE* 3.7 19.6 - - + +
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Residues in contact with THR 148 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108C THR* 3.6 33.9 - - + +
111C VAL* 4.5 1.4 - - + +
112C ALA* 4.1 6.5 - - + +
115C GLN* 2.8 23.2 + - - +
130C SER* 3.3 8.7 - - - -
131C THR* 2.6 51.5 + - - +
133C ILE* 4.2 5.8 - - + -
147C GLN* 1.3 88.1 - - - +
149C GLU* 1.3 63.1 + - - +
153C ILE 3.6 7.6 - - - -
154C TYR* 4.0 5.6 - - + -
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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