Contacts of the helix formed by residues 102 - 113 (chain D) in PDB entry 4GUN
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 SER 102 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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99D ASP* 2.6 28.8 + - - -
101D SER* 1.4 83.2 + - - +
103D ALA* 1.4 55.9 + - - +
104D LEU 3.9 1.6 + - - -
105D GLY 3.1 12.1 + - - -
106D LYS* 2.8 32.6 + - - +
201D GLU* 3.6 33.5 - - - +
302D SO4 3.5 21.3 - - - -
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Residues in contact with ALA 103 (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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101D SER 4.0 0.4 + - - -
102D SER* 1.4 68.9 - - - +
104D LEU* 1.4 56.3 + - - +
106D LYS* 3.6 14.4 + - - +
107D GLN* 3.1 28.8 + - - +
204D TYR* 3.7 20.4 - - + -
205D SER* 3.5 14.6 - - - +
302D SO4 2.7 21.2 + - - +
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Residues in contact with LEU 104 (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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98D PRO* 4.3 2.9 - - + -
102D SER* 3.3 3.4 + - - +
103D ALA* 1.4 74.1 - - - +
105D GLY* 1.3 61.0 + - - +
107D GLN* 3.0 3.6 + - - -
108D ILE* 2.9 40.5 + - + +
137D ILE* 5.4 2.0 - - + -
147D LEU* 3.9 23.1 - - + -
166D ILE* 4.1 11.2 - - + -
197D TRP* 4.2 15.0 - - + -
200D ALA* 3.7 37.7 - - + -
201D GLU* 3.7 18.1 + - + +
204D TYR* 3.7 38.5 - - + +
205D SER* 5.0 0.4 + - - -
302D SO4 4.6 0.2 + - - -
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Residues in contact with GLY 105 (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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98D PRO* 4.8 7.2 - - - +
99D ASP 3.3 22.0 - - - -
100D THR* 3.5 11.6 - - - +
102D SER* 3.1 10.7 + - - -
104D LEU* 1.3 75.6 - - - +
106D LYS* 1.3 60.4 + - - +
108D ILE* 3.5 10.7 + - - +
109D VAL* 3.2 30.0 + - - +
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Residues in contact with LYS 106 (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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100D THR 3.3 15.2 + - - +
101D SER* 3.7 20.9 - - - +
102D SER 2.8 23.2 + - - +
103D ALA* 3.7 9.6 - - - +
105D GLY* 1.3 73.8 - - - +
107D GLN* 1.3 57.0 + - - +
109D VAL* 3.5 6.0 + - - +
110D ALA* 3.0 28.6 + - - +
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Residues in contact with GLN 107 (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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103D ALA 3.1 16.6 + - - +
104D LEU 3.0 5.8 + - - +
106D LYS* 1.3 74.6 - - - +
108D ILE* 1.4 63.3 + - - +
110D ALA* 3.4 7.9 + - - +
111D GLN* 2.9 62.0 + - - +
144D GLY 4.4 8.7 + - - +
145D GLY 3.7 11.6 + - - +
146D ALA* 4.1 4.8 - - - +
147D LEU* 3.9 13.5 - - + -
204D TYR* 3.3 26.8 + - + +
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Residues in contact with ILE 108 (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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98D PRO* 3.7 29.4 - - + -
104D LEU* 2.9 32.9 + - + +
105D GLY* 3.8 5.6 - - - +
107D GLN* 1.4 74.0 - - - +
109D VAL* 1.4 58.5 + - + +
112D TYR* 2.8 35.3 + - + -
113D GLY 3.4 2.9 + - - -
114D SER* 3.7 7.4 - - - +
115D VAL* 3.7 39.0 - - + +
118D LEU* 3.8 24.9 - - + -
147D LEU* 3.8 19.5 - - + +
197D TRP* 4.2 6.3 - - + -
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Residues in contact with VAL 109 (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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100D THR* 4.1 27.4 - - + +
105D GLY 3.2 18.4 + - - +
106D LYS* 3.8 6.1 - - - +
107D GLN 3.3 0.2 - - - -
108D ILE* 1.4 79.0 - - + +
110D ALA* 1.3 63.2 + - - +
113D GLY* 3.0 38.6 + - - +
114D SER* 5.4 2.0 - - - -
115D VAL* 6.5 0.4 - - + -
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Residues in contact with ALA 110 (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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144A GLY* 5.3 2.4 - - - -
106D LYS 3.0 17.4 + - - +
107D GLN* 3.4 11.6 + - - +
109D VAL* 1.3 80.0 - - - +
111D GLN* 1.3 62.7 + - + +
113D GLY 4.9 0.2 + - - -
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Residues in contact with GLN 111 (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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142A GLN 3.8 2.6 - - - +
143A ASN* 2.9 56.1 + - - +
144A GLY* 3.2 8.8 + - - +
146A ALA* 4.2 3.2 - - - +
107D GLN* 2.9 44.5 + - - +
110D ALA* 1.3 77.2 - - + +
112D TYR* 1.3 69.3 + - + +
113D GLY 3.8 0.2 - - - -
146D ALA* 3.5 8.5 - - - +
147D LEU* 2.7 48.7 + - - +
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Residues in contact with TYR 112 (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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142A GLN* 3.7 8.7 - - + -
143A ASN* 3.4 24.7 - - + +
108D ILE* 2.8 28.8 + - - +
111D GLN* 1.3 81.2 - - + +
113D GLY* 1.3 54.9 + - - +
114D SER 3.0 21.8 + - - +
117D ASN* 3.0 26.4 + - - +
118D LEU* 3.7 36.4 - - + +
121D ILE* 3.6 35.9 - - + -
147D LEU* 3.4 43.9 + - + +
148D ASP* 3.6 12.3 + - - -
149D VAL* 4.3 2.3 + - - +
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Residues in contact with GLY 113 (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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108D ILE 3.4 0.8 + - - -
109D VAL* 3.0 38.5 + - - +
110D ALA 4.8 0.2 - - - -
111D GLN 3.8 0.8 - - - -
112D TYR* 1.3 74.1 - - - +
114D SER* 1.4 59.2 + - - +
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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