Contacts of the strand formed by residues 125 - 129 (chain K) in PDB entry 5O6I
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 125 (chain K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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114K TYR* 3.4 19.3 - - + +
122K LEU* 3.7 27.8 - - + +
124K ARG* 1.3 75.5 - - - +
126K ARG* 1.3 61.4 + - - +
164K ASN* 3.6 1.5 + - - +
165K ILE* 2.7 73.2 + - + +
166K SER 4.9 0.4 - - - +
167K LEU* 4.1 14.8 - - + +
170K ARG* 3.9 37.7 - - + +
173K PHE* 3.9 18.6 - - + -
174K VAL* 4.5 7.0 - - + -
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Residues in contact with ARG 126 (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* 3.5 5.2 + - - -
117K GLU 3.8 0.2 - - - +
118K GLY* 3.2 5.4 - - - -
119K ASP* 2.7 56.8 + - + +
121K THR* 5.9 0.2 - - - +
124K ARG* 3.5 36.0 - - + +
125K LEU* 1.3 77.6 - - - +
127K ILE* 1.3 65.3 + - - +
128K TRP* 3.4 33.2 - - + -
154K ASP* 5.2 1.2 + - - -
162K VAL* 3.8 18.6 - - + -
163K LEU 3.2 4.7 - - - -
164K ASN* 3.3 27.4 - - - +
7L C 3.9 5.3 - - - +
8L C 4.8 1.4 - - - +
17N C 3.9 4.6 - - - +
18N G 2.9 46.5 + - - -
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Residues in contact with ILE 127 (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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110K ILE* 4.8 9.0 - - + -
113K LEU* 4.2 17.5 - - + +
114K TYR* 3.5 32.8 - - + +
117K GLU* 3.7 22.7 - - + -
118K GLY* 4.6 0.9 - - - -
126K ARG* 1.3 79.9 - - - +
128K TRP* 1.3 65.5 + - - +
129K ASN* 5.5 0.7 - - + -
135K LEU* 3.9 19.5 - - + +
138K VAL* 4.7 20.9 - - + -
142K LEU* 5.3 0.4 - - + -
162K VAL* 3.2 3.4 - - - -
163K LEU* 2.7 50.9 + - + +
165K ILE* 4.4 12.8 - - + -
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Residues in contact with TRP 128 (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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117K GLU* 3.3 43.6 + - - +
118K GLY 4.1 0.4 - - - -
119K ASP* 3.8 26.0 - - + -
126K ARG* 3.4 55.2 - - + -
127K ILE* 1.3 76.6 - - - +
129K ASN* 1.3 65.3 + - - +
154K ASP* 3.0 26.0 + - + -
155K ASP* 6.3 0.4 - - + -
160K VAL* 4.0 12.8 - - + -
161K TYR 3.4 7.4 - - - -
162K VAL* 3.7 20.2 - - + +
15N C 3.4 24.5 - - + +
16N C 3.6 45.1 - + + -
17N C 3.7 18.8 - + - +
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Residues in contact with ASN 129 (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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19K ILE* 4.7 6.5 + - - +
113K LEU* 5.0 2.3 - - + +
117K GLU* 2.4 31.9 + - + +
127K ILE* 5.5 0.2 - - + -
128K TRP* 1.3 73.3 - - - +
130K LYS* 1.3 63.3 + - - +
131K ASN* 2.9 36.0 + - - +
134K LEU* 4.5 14.4 - - + +
135K LEU* 3.8 24.1 - - + +
160K VAL* 3.9 3.5 - - - +
161K TYR* 2.9 34.6 + - - +
202K MN 3.7 2.2 + - - -
15N C 3.2 17.5 + - - -
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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