Contacts of the strand formed by residues 135 - 139 (chain U) in PDB entry 5LN3
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 THR 135 (chain U).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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11U VAL* 5.1 6.7 - - + -
16U LEU* 3.9 27.4 - - + +
122U VAL* 4.7 12.1 - - + -
123U ILE 3.7 12.1 - - - +
124U ILE* 4.1 20.8 - - + +
133U LEU* 3.2 32.8 - - - +
134U PRO* 1.4 89.9 + - - +
136U GLU* 1.4 69.0 + - - +
137U ALA* 6.2 0.2 - - + -
160U SER* 4.2 10.6 + - - +
216V MET* 4.6 3.6 - - - +
220V LEU* 6.1 0.2 - - - +
234V TYR* 3.9 8.3 - - - -
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Residues in contact with GLU 136 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122U VAL* 3.7 1.4 - - - +
123U ILE* 2.7 72.0 + - + +
124U ILE* 5.1 0.2 - - - -
125U ASP* 5.2 1.6 + - - +
129U LYS* 4.6 18.7 + - - +
130U ASP* 5.7 2.8 - - - +
133U LEU 4.7 1.0 - - - +
134U PRO* 3.7 14.3 - - - +
135U THR* 1.4 78.3 - - - +
137U ALA* 1.3 58.7 + - - +
138U TYR* 3.7 24.7 - - + +
160U SER* 5.3 0.9 - - - -
234V TYR* 3.4 42.7 - - + +
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Residues in contact with ALA 137 (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 13.2 - - + -
120U VAL* 4.2 7.6 - - + -
121U LEU 3.7 4.7 - - - -
122U VAL* 3.9 19.5 - - + -
135U THR* 6.2 0.4 - - + -
136U GLU* 1.3 72.1 - - - +
138U TYR* 1.3 68.6 + - - +
156U GLU 3.1 13.0 - - - +
158U VAL* 3.7 23.4 - - + +
160U SER* 4.7 13.9 - - - +
234V TYR* 3.5 11.1 + - - -
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Residues in contact with TYR 138 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
443P THR* 3.7 14.9 - - + +
444P HIS* 3.9 18.2 - + - -
101U LEU* 6.0 4.0 - - + -
120U VAL* 3.6 4.6 - - - +
121U LEU* 2.8 41.3 + - + +
123U ILE* 4.0 21.8 - - + -
136U GLU* 3.7 25.2 - - + +
137U ALA* 1.3 72.7 - - - +
139U ILE* 1.4 64.7 + - - +
140U SER* 5.6 1.3 - - - -
155U PHE* 3.8 26.5 - + + -
156U GLU* 2.9 37.7 - - - +
157U HIS* 4.4 0.9 - - - -
158U VAL* 4.7 0.7 - - - -
234V TYR* 3.3 35.1 + - - -
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Residues in contact with ILE 139 (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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7U GLN* 4.3 24.5 - - + -
48U LEU* 4.5 13.2 - - + -
118U ASN* 5.0 16.2 - - + +
119U SER 3.7 20.6 - - - +
120U VAL* 4.2 18.6 - - + +
138U TYR* 1.4 78.4 - - - +
140U SER* 1.3 65.3 + - - +
141U VAL* 5.5 4.7 - - + -
154U THR* 3.7 3.0 + - - +
155U PHE* 3.5 23.2 + - - -
156U GLU* 3.3 43.0 - - - +
158U VAL* 4.4 15.3 - - + -
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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