Contacts of the strand formed by residues 162 - 166 (chain E) 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 ILE 162 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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129D PRO 6.1 0.4 - - - +
175D ILE 3.6 1.4 - - - +
176D ILE* 3.6 0.6 - - - -
177D ASN* 2.7 46.7 + - + +
180D ARG* 4.1 27.1 - - + +
181D GLU* 3.6 39.0 - - + +
146E LEU* 3.9 13.5 - - + -
154E THR* 3.6 24.7 - - + -
155E MET 3.4 9.9 - - - +
156E ARG* 3.9 17.0 - - + -
160E GLY 3.9 0.2 + - - -
161E LYS* 1.3 70.1 - - - +
163E ILE* 1.3 61.3 + - - +
164E VAL* 4.2 9.8 + - + +
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Residues in contact with ILE 163 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174D ASN* 4.4 13.5 - - + -
175D ILE 3.3 7.4 - - - +
176D ILE* 4.0 27.1 - - + -
141E VAL* 3.2 31.9 - - + -
153E THR 3.8 0.9 - - - +
154E THR* 3.4 4.7 - - - +
155E MET* 2.9 42.6 + - + +
157E THR* 3.4 32.1 - - + -
161E LYS* 4.6 1.1 - - - +
162E ILE* 1.3 78.1 - - - +
164E VAL* 1.3 66.1 + - - +
165E ILE* 3.8 21.5 - - + -
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Residues in contact with VAL 164 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129D PRO* 4.4 30.1 - - + +
173D GLY 4.1 0.5 - - - +
174D ASN* 3.6 3.3 - - - -
175D ILE* 2.8 46.8 + - + +
177D ASN* 6.1 1.1 - - + -
152E SER* 3.8 25.8 - - - +
153E THR 3.5 4.7 - - - +
154E THR* 4.2 21.5 - - + +
162E ILE* 4.3 8.3 - - + -
163E ILE* 1.3 78.2 - - - +
165E ILE* 1.3 64.1 + - - +
166E PRO* 4.0 3.3 - - - +
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Residues in contact with ILE 165 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174D ASN* 3.3 23.6 - - - +
138E LEU* 4.1 28.5 - - + +
141E VAL* 4.4 8.1 - - + -
152E SER* 3.2 3.0 - - - -
153E THR* 2.9 35.3 + - + +
155E MET* 3.8 28.0 - - + -
163E ILE* 3.8 14.8 - - + +
164E VAL* 1.3 77.2 - - - +
166E PRO* 1.3 70.9 - - + +
169E LYS* 4.1 13.5 - - + +
170E ILE* 3.5 26.7 - - + +
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Residues in contact with PRO 166 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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171D ILE 3.8 16.2 - - - +
172D ALA* 3.7 23.8 - - - +
173D GLY 3.4 20.4 - - - +
174D ASN* 4.3 0.2 - - - +
117E ASN* 3.5 19.7 - - - +
151E PHE 3.8 6.5 - - - +
152E SER* 3.9 4.9 - - - -
164E VAL 4.0 2.0 - - - +
165E ILE* 1.3 87.4 - - + +
167E ASN* 1.3 66.1 + - - +
169E LYS* 3.1 26.2 + - + +
170E ILE* 3.2 10.7 + - - +
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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