Contacts of the helix formed by residues 117 - 122 (chain A) in PDB entry 5H8N
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 ASN 117 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115A THR* 3.5 5.4 + - + +
116A ILE* 1.3 75.9 - - - +
118A GLU* 1.3 60.2 + - - +
119A GLU* 3.5 15.9 + - - +
120A ARG* 3.0 43.2 + - - +
121A SER* 2.7 31.3 + - - -
126A PHE* 4.4 2.2 - - - -
172A SER* 3.6 30.4 + - - +
175A ARG* 5.0 6.2 - - - +
270B LEU* 3.9 6.1 - - - -
274B GLU* 3.3 20.0 - - + +
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Residues in contact with GLU 118 (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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117A ASN* 1.3 72.2 - - - +
119A GLU* 1.4 63.7 + - - +
121A SER 3.2 9.7 + - - -
122A GLU* 3.3 28.6 + - - +
267B LEU* 3.6 28.6 - - + +
270B LEU* 4.1 18.1 - - + +
271B LYS* 3.3 39.5 - - - +
274B GLU* 2.8 25.0 + - - +
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Residues in contact with GLU 119 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89A LYS* 5.7 0.7 - - - -
90A LYS* 4.7 16.8 + - - +
95A TRP* 3.4 38.1 - - + -
117A ASN* 3.5 15.3 + - - +
118A GLU* 1.4 77.9 - - - +
120A ARG* 1.3 64.0 + - - +
122A GLU* 3.4 29.8 + - - +
123A VAL* 4.0 5.0 + - - +
175A ARG* 2.8 51.6 + - + +
274B GLU* 5.1 0.8 + - - -
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Residues in contact with ARG 120 (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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87A HIS* 3.9 0.2 - - - +
88A GLY 2.9 37.2 + - - +
95A TRP* 3.6 20.9 - - + -
99A ILE* 3.9 20.3 - - + +
114A LEU* 3.5 13.4 - - - +
115A THR* 3.0 29.1 + - - +
117A ASN* 3.0 30.5 + - - +
119A GLU* 1.3 75.9 + - - +
121A SER* 1.4 56.3 + - - +
123A VAL* 3.1 14.3 + - - +
124A VAL* 3.1 28.1 + - - +
126A PHE* 3.7 17.0 - - + -
171A GLY* 4.4 1.8 - - - -
172A SER* 4.0 9.6 - - - +
301A GLU* 3.0 40.0 + - - -
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Residues in contact with SER 121 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116A ILE* 4.0 1.0 - - - +
117A ASN 2.7 23.9 + - - -
118A GLU 3.2 5.3 + - - -
120A ARG* 1.4 71.9 - - - +
122A GLU* 1.3 58.8 + - - +
123A VAL 3.3 0.4 - - - -
124A VAL 3.2 10.0 - - - +
125A ASP* 5.1 0.3 - - - +
126A PHE* 3.2 21.4 - - - -
250A LYS* 2.9 20.6 + - - -
140B LYS* 5.4 1.7 - - - -
263B GLN* 3.2 10.5 + - - -
267B LEU* 3.8 14.8 - - - -
270B LEU* 3.4 17.5 - - - +
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Residues in contact with GLU 122 (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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90A LYS* 5.7 3.6 + - - -
118A GLU* 3.3 32.2 + - - +
119A GLU* 3.5 19.0 - - - +
120A ARG 3.2 0.6 - - - -
121A SER* 1.3 77.5 - - - +
123A VAL* 1.4 64.4 + - + +
250A LYS* 3.5 18.3 + - - +
263B GLN* 4.5 4.7 + - - +
267B LEU* 4.1 18.2 - - + +
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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