Contacts of the strand formed by residues 89 - 93 (chain M) 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 LEU 89 (chain M).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121H PHE* 3.4 30.1 - - + -
87M PRO 6.1 0.4 - - - -
88M TYR* 1.4 81.6 - - - +
90M VAL* 1.3 61.6 + - - +
91M SER* 4.5 3.1 - - - +
126M THR* 3.3 27.6 - - + +
128M THR* 6.3 1.1 - - + -
153M VAL* 3.3 34.5 + - + +
155M LYS* 4.2 29.1 - - + +
158M TYR* 4.4 17.0 - - + +
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Residues in contact with VAL 90 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120H LYS* 5.5 4.7 - - + +
121H PHE* 3.5 34.0 - - + -
122H VAL* 4.3 30.1 - - + +
123H VAL 5.1 2.2 - - - +
124H ASP* 4.6 3.1 - - - +
88M TYR* 4.2 20.2 - - + +
89M LEU* 1.3 77.2 - - - +
91M SER* 1.4 64.2 + - - +
126M THR* 4.2 1.4 + - - -
127M SER* 3.8 11.2 + - - +
150M LEU* 5.1 10.5 - - + -
151M VAL 3.7 5.8 - - - -
152M GLY* 4.8 0.2 - - - -
164M LEU* 4.2 24.2 - - + -
168M TYR* 6.4 0.2 - - + -
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Residues in contact with SER 91 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89M LEU* 4.5 3.3 - - - +
90M VAL* 1.4 77.2 + - - +
92M ASN* 1.3 60.9 + - - +
124M ILE* 3.9 22.9 - - - +
125M LYS 3.7 14.6 - - - -
126M THR* 3.3 22.2 + - - -
127M SER* 5.2 1.6 - - - -
150M LEU* 3.5 11.7 - - - +
151M VAL* 3.2 30.4 + - - +
153M VAL* 4.0 17.8 - - - +
168M TYR* 5.8 0.7 - - - -
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Residues in contact with ASN 92 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91M SER* 1.3 77.2 - - - +
93M VAL* 1.3 67.5 + - - +
94M ILE* 3.4 20.5 + - + +
124M ILE* 3.3 3.0 - - - -
125M LYS* 3.1 30.3 + - + +
148M GLY* 4.2 7.2 - - - -
149M ASP 3.3 26.1 + - - +
150M LEU* 4.7 0.2 - - + -
168M TYR* 3.7 55.9 - - + +
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Residues in contact with VAL 93 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92M ASN* 1.3 75.5 - - - +
94M ILE* 1.4 55.6 + - - +
95M GLU 3.4 28.7 - - - +
96M LEU* 4.3 6.3 - - + +
122M ALA* 4.9 5.2 - - + -
123M VAL 3.3 12.1 - - - +
124M ILE* 3.9 6.5 - - + -
145M LEU* 4.8 6.5 - - + -
146M LYS 3.9 16.8 - - - +
148M GLY* 2.9 27.4 + - - -
149M ASP* 2.8 15.0 + - + +
151M VAL* 3.4 39.7 - - + -
160M ILE* 4.7 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