Contacts of the strand formed by residues 160 - 165 (chain K) in PDB entry 5AKM
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 VAL 160 (chain K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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128K TRP* 3.9 15.0 - - + -
129K ASN 3.8 9.0 - - - +
130K LYS* 4.4 0.9 - - - +
153K LEU* 3.4 4.0 - - - +
154K ASP* 3.0 6.1 + - - -
155K ASP* 2.8 41.2 + - + -
158K HIS* 4.0 8.7 - - + +
159K GLY* 1.3 80.2 - - - +
161K TYR* 1.3 72.9 + - - +
14N A 3.8 15.5 - - + +
15N C 3.5 60.6 - - + +
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Residues in contact with TYR 161 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128K TRP* 3.3 3.8 - - - -
129K ASN 2.8 37.8 + - - +
130K LYS 3.9 19.1 - - - -
132K LYS* 3.4 56.4 + - + +
135K LEU* 3.8 15.6 - - + +
151K ILE* 4.3 6.1 - - + -
152K HIS* 3.4 23.3 - - - +
153K LEU* 3.5 34.6 - - + +
154K ASP* 4.4 0.7 - - - -
159K GLY* 4.2 5.2 - - - -
160K VAL* 1.3 76.4 - - - +
162K VAL* 1.3 61.1 + - - +
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Residues in contact with VAL 162 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126K ARG* 3.7 31.0 - - + -
127K ILE 3.4 10.1 - - - +
128K TRP* 3.6 25.8 - - + +
135K LEU* 4.1 3.6 - - - -
150K THR 3.8 0.7 - - - +
151K ILE* 3.3 5.4 - - - +
152K HIS* 2.9 40.6 + - + +
154K ASP* 3.6 25.9 - - + +
161K TYR* 1.3 73.9 - - - +
163K LEU* 1.3 65.7 + - - +
164K ASN* 4.4 7.9 - - + +
6L G 5.6 3.6 - - - +
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Residues in contact with LEU 163 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126K ARG* 3.2 4.7 - - - -
127K ILE* 2.7 45.1 + - + +
135K LEU* 3.6 43.2 - - + +
138K VAL* 3.8 24.5 - - + -
139K SER* 3.9 11.2 - - - +
142K LEU* 3.9 6.3 - - + -
149K ASN* 3.6 30.3 - - + +
150K THR 3.4 7.9 - - - +
151K ILE* 4.1 5.6 - - + -
162K VAL* 1.3 73.4 - - - +
164K ASN* 1.3 58.7 + - - +
165K ILE* 3.7 21.6 + - + +
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Residues in contact with ASN 164 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124K ARG* 4.7 9.1 + - - +
125K LEU 3.7 3.9 + - - +
126K ARG* 3.4 25.5 - - + +
149K ASN* 3.1 5.0 - - - +
150K THR* 2.8 43.3 + - - +
152K HIS* 5.9 0.4 - - + -
162K VAL* 3.8 8.3 + - + -
163K LEU* 1.3 73.7 - - - +
165K ILE* 1.3 70.0 + - - +
166K SER* 4.6 1.2 - - - +
5L T 3.7 40.9 + - - +
6L G 3.7 18.8 - - - +
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Residues in contact with ILE 165 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114K TYR* 4.6 0.2 - - + -
125K LEU* 2.7 56.9 + - + +
127K ILE* 4.4 13.7 - - + -
142K LEU* 4.3 4.5 - - + -
147K VAL* 3.5 26.0 - - + -
148K ARG 3.9 2.9 - - - -
149K ASN* 4.3 1.1 - - + -
163K LEU* 3.7 27.4 - - + +
164K ASN* 1.3 79.5 + - - +
166K SER* 1.3 74.5 + - - +
167K LEU* 3.2 6.1 + - - +
169K ASP 5.0 0.9 - - - +
173K PHE* 4.0 38.8 - - + -
5L T 4.0 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