Contacts of the strand formed by residues 120 - 124 (chain U) in PDB entry 5L4K
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 120 (chain U).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6U VAL* 4.5 3.8 - - + -
9U VAL* 4.8 11.9 - - + -
39U LEU* 4.8 2.6 - - + +
48U LEU* 3.4 26.9 - - + -
50U VAL* 5.9 1.6 - - + -
92U VAL 3.6 15.5 - - - +
93U GLY* 3.6 3.1 - - - -
94U TRP* 3.0 28.6 + - - +
118U ASN 3.3 16.4 - - - +
119U SER* 1.3 74.9 - - - +
121U LEU* 1.3 65.5 + - - +
122U VAL* 4.1 17.0 + - + -
138U TYR 3.3 17.0 - - - +
139U ILE* 3.9 18.2 - - + +
158U VAL* 5.8 0.2 - - + -
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Residues in contact with LEU 121 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94U TRP* 3.2 53.2 - - + +
96U HIS* 4.4 2.5 - - + -
101U LEU* 4.7 6.5 - - + -
105U ASP* 3.8 24.0 - - + +
109U ASN* 3.8 9.4 - - - +
120U VAL* 1.3 75.1 - - - +
122U VAL* 1.3 69.8 + - - +
123U ILE* 4.0 15.0 - - + +
137U ALA* 3.3 3.6 - - - +
138U TYR* 3.0 43.4 + - + +
140U SER 5.8 0.2 - - - +
155U PHE* 3.6 31.9 - - + -
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Residues in contact with VAL 122 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9U VAL* 4.2 24.7 - - + -
11U VAL* 4.2 19.7 - - + -
39U LEU* 3.5 29.8 - - + -
94U TRP 3.5 6.7 + - - -
95U TYR* 3.4 20.3 - - + +
96U HIS 3.8 2.1 + - - +
120U VAL* 4.3 5.8 - - + -
121U LEU* 1.3 81.5 - - - +
123U ILE* 1.3 62.6 - - - +
124U ILE* 3.1 26.9 + - + +
135U THR* 4.9 8.1 - - - -
136U GLU 3.4 7.4 - - - +
137U ALA* 4.6 3.8 - - + -
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Residues in contact with ILE 123 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96U HIS* 3.3 37.7 - - + +
98U GLY* 3.7 23.6 - - - +
99U PRO 4.5 8.1 - - - +
100U LYS* 4.7 8.1 - - - +
101U LEU* 4.2 15.7 - - + -
105U ASP* 4.7 0.2 - - - +
121U LEU* 4.4 7.9 - - + -
122U VAL* 1.3 68.9 - - - +
124U ILE* 1.3 61.8 + - - +
125U ASP* 4.4 9.3 - - - +
134U PRO 3.5 1.6 - - - +
135U THR* 3.4 6.6 + - - -
136U GLU* 2.9 42.2 + - + +
138U TYR* 3.7 29.6 - - + +
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Residues in contact with ILE 124 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11U VAL* 5.1 0.9 - - + -
15U VAL* 4.5 10.8 - - + -
16U LEU* 4.0 18.6 - - + -
19U VAL* 3.5 47.3 - - + -
39U LEU* 5.7 0.4 - - + -
95U TYR* 4.6 7.2 - - + -
96U HIS 3.8 3.2 + - - +
97U THR* 3.3 30.5 - - - +
98U GLY* 3.6 1.2 + - - -
122U VAL* 3.1 31.1 + - + +
123U ILE* 1.3 75.6 - - - +
125U ASP* 1.3 75.6 + - - +
134U PRO 3.3 12.6 - - - +
135U THR* 4.3 4.0 - - + -
216V MET* 4.0 14.4 - - + -
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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