Contacts of the strand formed by residues 152 - 156 (chain A) in PDB entry 5AJI
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 SER 152 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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149A GLN* 2.8 43.5 + - - +
151A PHE* 1.3 84.9 - - - +
153A THR* 1.3 56.2 + - - +
154A THR* 5.1 1.1 + - - -
164A VAL* 3.8 19.3 - - - +
165A ILE 3.2 16.2 - - - -
166A PRO* 3.9 6.5 - - - -
167A ASN* 3.3 13.4 - - - +
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Residues in contact with THR 153 (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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124A LEU* 4.1 2.4 - - - +
130A PHE* 4.2 15.9 - - + -
138A LEU* 4.9 6.1 - - + -
145A VAL* 4.2 7.4 - - + -
147A SER 3.4 13.9 - - - +
148A VAL* 3.6 22.9 - - + +
152A SER* 1.3 73.7 - - - +
154A THR* 1.3 70.9 + - - +
155A MET* 5.5 2.4 - - + +
163A ILE 3.8 0.7 - - - +
164A VAL* 3.5 2.8 - - - -
165A ILE* 2.9 33.6 + - + +
167A ASN* 2.8 19.2 + - - -
170A ILE* 3.4 21.5 - - + +
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Residues in contact with THR 154 (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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145A VAL* 3.8 1.7 - - - -
146A LEU* 2.8 39.1 + - + -
147A SER* 3.1 19.6 + - - +
149A GLN* 3.7 13.9 + - - -
152A SER* 4.8 1.0 + - - -
153A THR* 1.3 77.5 + - - +
155A MET* 1.3 64.8 + - - +
162A ILE* 3.5 28.9 - - + -
163A ILE 3.4 4.9 - - - +
164A VAL* 4.2 13.1 - - + +
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Residues in contact with MET 155 (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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136A VAL* 4.2 4.3 - - - +
138A LEU* 4.7 11.7 - - - -
141A VAL* 3.6 15.7 - - + +
142A ALA* 2.9 18.8 - - - +
143A GLY* 2.8 44.2 - - - +
144A THR 3.3 18.2 - - - +
145A VAL* 4.1 4.9 - - + -
146A LEU* 4.1 5.8 - - - -
153A THR* 5.5 3.1 - - + +
154A THR* 1.3 74.8 - - - +
156A ARG* 1.3 61.1 + - - +
157A THR* 5.1 0.7 - - + -
161A LYS 3.7 0.2 - - - +
162A ILE* 3.4 6.6 - - - +
163A ILE* 3.0 47.3 + - + +
165A ILE* 3.8 25.8 - - + -
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Residues in contact with ARG 156 (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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143A GLY* 3.3 1.5 - - - -
144A THR* 2.9 46.9 + - - +
146A LEU* 3.8 33.2 - - + +
155A MET* 1.3 72.8 - - - +
157A THR* 1.3 75.1 + - - +
160A GLY* 4.0 18.2 - - - -
161A LYS 3.3 9.6 - - - +
162A ILE* 3.9 16.5 - - + +
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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