Contacts of the helix formed by residues 116 - 125 (chain D) in PDB entry 4OA5
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 GLU 116 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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89D LYS* 4.0 20.9 + - + +
115D GLY* 1.3 73.9 - - - -
117D ALA* 1.3 65.2 + - - +
118D LEU* 4.6 1.3 - - + +
119D ALA* 3.2 8.8 + - + +
120D GLN* 3.0 18.4 + - - +
301D SAH 3.4 23.2 + - - -
304D IOD 3.7 13.7 - - + +
305D IOD 3.5 20.4 - - + +
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Residues in contact with ALA 117 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63D VAL* 3.6 24.5 - - + -
87D ILE* 3.7 14.1 - - + -
116D GLU* 1.3 71.5 - - - +
118D LEU* 1.3 58.6 + - - +
120D GLN* 3.2 0.7 + - - +
121D LEU* 2.7 39.4 + - + +
145D TYR* 3.4 23.3 - - + +
301D SAH 2.8 25.1 + - + +
304D IOD 4.0 1.0 - - - +
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Residues in contact with LEU 118 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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181A SER* 3.9 13.8 + - - +
182A ASN* 3.4 41.5 - - - +
319A IOD 3.7 21.5 - - + -
116D GLU* 3.3 1.2 + - + -
117D ALA* 1.3 76.1 - - - +
119D ALA* 1.3 62.3 + - - +
121D LEU* 3.5 9.2 + - + +
122D ASN* 3.2 26.9 + - - +
141D SER* 4.2 1.6 - - - +
144D ALA* 3.8 25.6 - - + +
145D TYR* 3.8 17.7 - - + -
148D TRP* 5.8 2.2 - - + -
304D IOD 3.4 27.8 - - + +
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Residues in contact with ALA 119 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116D GLU* 3.2 12.8 + - + +
118D LEU* 1.3 80.7 - - - +
120D GLN* 1.3 64.5 + - - +
122D ASN* 3.2 24.0 + - - +
123D THR* 3.4 12.0 + - - +
305D IOD 3.9 24.2 - - + -
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Residues in contact with GLN 120 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87D ILE* 3.7 33.9 - - + -
113D LEU* 3.6 21.7 - - + +
114D HIS 3.7 7.7 + - - +
115D GLY* 3.8 17.9 - - - +
116D GLU 3.0 16.5 + - - +
119D ALA* 1.3 77.7 + - - +
121D LEU* 1.3 65.5 + - - +
123D THR* 2.8 39.1 + - - +
124D LEU* 3.2 9.4 + - - +
305D IOD 4.4 4.9 - - - +
155E LYS* 3.2 42.4 + - - +
218E THR* 4.9 1.4 + - - -
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Residues in contact with LEU 121 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61D VAL* 3.6 31.2 - - + -
63D VAL* 4.4 10.3 - - + -
87D ILE* 3.7 12.1 - - + -
117D ALA 2.7 26.8 + - - +
118D LEU* 3.8 9.4 - - + +
120D GLN* 1.3 72.7 - - - +
122D ASN* 1.3 61.6 + - - +
124D LEU* 3.1 15.1 + - + +
125D LYS 3.3 6.4 + - - -
133D ILE* 4.8 1.1 - - + -
145D TYR* 3.8 30.7 - - + -
148D TRP* 3.1 61.3 + - + +
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Residues in contact with ASN 122 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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177A GLU* 5.1 14.5 - - - +
181A SER* 5.1 8.9 + - - -
118D LEU 3.2 20.3 + - - +
119D ALA* 3.3 15.9 - - - +
120D GLN 3.1 0.8 - - - -
121D LEU* 1.3 75.6 - - - +
123D THR* 1.3 61.0 + - + +
125D LYS* 2.9 54.6 + - - +
126D GLU 4.8 0.2 + - - -
148D TRP* 5.1 3.5 - - - -
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Residues in contact with THR 123 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113D LEU* 4.3 4.9 - - - +
119D ALA 3.6 13.2 - - - +
120D GLN* 2.8 34.7 + - - +
122D ASN* 1.3 77.9 - - + +
124D LEU* 1.3 65.5 + - - +
125D LYS 3.4 0.5 + - - -
126D GLU* 4.0 8.1 + - - +
127D MET* 3.5 16.1 - - - +
129E PRO* 5.8 1.9 - - - +
151E MET 5.0 8.9 - - - +
155E LYS* 5.8 2.7 - - + +
216E LYS* 6.1 1.3 - - - +
218E THR* 4.5 15.5 - - - +
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Residues in contact with LEU 124 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61D VAL* 4.0 25.6 - - + -
85D TYR* 3.9 38.1 - - + -
87D ILE* 4.3 10.3 - - + -
113D LEU* 3.8 26.2 - - + -
120D GLN 3.2 10.7 + - - +
121D LEU* 3.1 11.9 + - + +
123D THR* 1.3 80.0 + - - +
125D LYS* 1.3 63.7 + - - +
126D GLU 3.0 3.1 - - - -
127D MET* 3.0 32.2 + - + +
130D PHE* 3.5 28.1 - - + -
148D TRP* 4.3 4.0 - - + -
129E PRO* 4.3 3.6 - - + -
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Residues in contact with LYS 125 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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175A PRO 5.0 9.9 + - - -
176A THR 5.7 0.2 - - - -
177A GLU* 5.3 11.3 - - - +
199C LYS* 3.6 10.5 + - - -
218C THR* 6.3 1.8 - - - -
121D LEU 3.3 9.2 + - - +
122D ASN* 2.9 47.9 + - - +
123D THR 3.3 1.4 - - - -
124D LEU* 1.3 77.7 - - - +
126D GLU* 1.3 63.1 + - - +
128D ALA* 3.1 23.8 + - - +
148D TRP* 4.0 7.0 - - - +
152D TYR* 3.4 49.3 - - + +
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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