Contacts of the strand formed by residues 149 - 152 (chain A) in PDB entry 5T0I
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 ILE 149 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100A LYS* 4.3 0.7 - - - +
111A TYR* 4.4 11.9 - - + -
113A ILE* 3.7 31.0 - - + -
123A VAL* 4.0 3.1 - - + +
124A ASP 3.4 9.9 + - - +
125A LEU* 3.8 36.7 - - + +
126A SER* 3.2 27.0 + - - -
129A VAL* 5.4 6.4 - - + +
134A ILE* 4.3 20.2 - - + -
140A VAL* 3.7 32.8 - - + -
141A GLY 3.5 5.2 - - - -
148A GLN* 1.3 76.4 - - - +
150A HIS* 1.3 67.4 + - - +
151A ILE 5.3 0.9 - - - -
152A PRO* 5.5 0.7 - - + -
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Residues in contact with HIS 150 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92A PRO* 6.0 0.4 - - - +
93A LEU* 3.4 46.3 + - + +
95A VAL* 4.9 10.1 - - + -
96A ALA* 5.7 3.4 - - + +
126A SER* 4.2 4.4 + - - -
128A GLN* 5.7 0.9 - - - +
129A VAL* 3.3 23.7 - - - +
141A GLY* 3.0 10.5 + - - -
142A VAL* 3.5 31.9 - - - +
143A ASP* 5.3 5.6 - - + -
148A GLN* 5.9 4.0 - - + -
149A ILE* 1.3 75.8 - - - +
151A ILE* 1.3 74.9 + - + +
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Residues in contact with ILE 151 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93A LEU* 5.1 4.9 - - + -
129A VAL* 5.1 5.8 - - + -
140A VAL* 4.1 2.0 - - - -
141A GLY* 2.3 34.5 + - - +
150A HIS* 1.3 102.9 - - + +
152A PRO* 1.3 85.0 - - + +
153A LEU 3.7 0.2 + - - -
132B TYR* 3.8 30.2 + - + +
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Residues in contact with PRO 152 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129A VAL* 4.7 20.9 - - + -
133A ASP* 5.6 7.6 - - + +
134A ILE* 5.3 4.0 - - + -
138A MET* 3.8 20.9 - - + -
140A VAL* 3.7 25.8 - - + -
149A ILE* 5.7 0.9 - - + -
151A ILE* 1.3 108.2 - - + +
153A LEU* 1.3 59.8 + - - +
154A PRO* 3.8 6.9 - - - +
132B TYR* 4.8 1.0 + - - -
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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