Contacts of the helix formed by residues 109 - 123 (chain D) in PDB entry 2NS8
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 GLN 109 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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57D ILE* 3.6 21.3 - - - +
60D LEU* 5.5 9.1 - - - +
103D THR* 5.7 3.2 - - - +
105D PRO* 3.8 25.6 - - + +
106D THR* 3.0 11.7 + - - +
108D LYS* 1.3 108.5 + - + +
110D TYR* 1.3 60.3 + - - +
111D GLU 3.2 0.7 - - - -
112D THR* 3.0 17.8 + - - +
113D LEU* 2.8 43.0 + - + +
1G TRP* 6.4 0.4 - - - +
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Residues in contact with TYR 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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162C THR* 3.3 28.6 - - - +
165C SER* 3.4 29.2 - - - -
166C MET* 3.4 36.2 - - + +
167C PRO* 3.8 30.9 - - + +
170C LEU* 4.0 15.6 - - + +
105D PRO 4.0 9.9 + - - -
106D THR* 3.3 24.9 - - - -
107D GLU* 3.3 22.0 + - - +
108D LYS 3.1 0.4 - - - -
109D GLN* 1.3 77.0 - - - +
111D GLU* 1.3 55.0 + - - +
113D LEU* 4.5 4.9 - - + -
114D GLU* 2.7 40.7 + - - +
8G PHE* 4.1 8.0 - + - -
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Residues in contact with GLU 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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167C PRO* 5.0 2.0 - - - +
108D LYS 3.5 14.2 + - - +
110D TYR* 1.3 77.0 - - - +
112D THR* 1.3 66.2 + - - +
114D GLU* 3.8 3.9 - - - +
115D ASN* 3.0 51.5 + - - +
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Residues in contact with THR 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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67D PHE* 3.6 50.8 - - + +
68D SER* 3.7 8.9 + - - +
108D LYS 4.9 0.7 + - - -
109D GLN* 3.0 20.5 + - - +
111D GLU* 1.3 79.9 - - - +
113D LEU* 1.3 66.7 + - + +
115D ASN* 3.1 9.2 + - - +
116D GLN* 3.1 25.8 + - - +
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Residues in contact with LEU 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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170C LEU* 4.5 20.0 - - + -
105D PRO* 3.9 27.6 - - + -
109D GLN* 2.8 31.2 + - + +
110D TYR* 3.9 4.5 - - + +
112D THR* 1.3 74.2 - - + +
114D GLU* 1.3 66.5 + - - +
116D GLN* 3.1 25.3 + - - +
117D LEU* 3.1 16.9 + - - +
0G ACE 5.9 0.4 - - - -
1G TRP* 3.9 34.3 - - + +
3G TRP* 3.7 29.8 - - + +
8G PHE* 5.5 1.1 - - + -
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Residues in contact with GLU 114 (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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167C PRO* 3.4 27.9 - - + +
168C PRO* 3.6 11.5 - - + +
169C LEU* 3.2 33.9 + - + +
170C LEU* 2.9 31.1 + - + +
110D TYR 2.7 23.0 + - - +
111D GLU* 3.8 4.9 - - - +
113D LEU* 1.3 71.6 - - - +
115D ASN* 1.3 59.4 + - - +
117D LEU* 3.4 7.3 + - - +
118D ALA* 2.9 30.9 + - + +
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Residues in contact with ASN 115 (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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68D SER* 4.4 12.8 - - - +
69D PRO* 4.3 7.9 - - + +
111D GLU* 3.0 42.6 + - - +
112D THR* 3.1 12.0 + - - +
114D GLU* 1.3 75.6 - - - +
116D GLN* 1.3 65.8 + - - +
118D ALA* 3.8 6.3 - - - +
119D PHE* 2.9 27.8 + - - +
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Residues in contact with GLN 116 (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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64D HIS* 5.1 2.2 + - - -
67D PHE* 2.6 28.4 + - - +
69D PRO* 4.4 7.0 - - + -
78D PHE* 3.6 18.9 - - + -
82D ASN* 3.5 17.6 + - - +
112D THR* 3.1 18.5 + - - +
113D LEU* 3.1 16.6 + - - +
115D ASN* 1.3 75.7 - - - +
117D LEU* 1.3 64.0 + - - +
119D PHE* 3.5 4.6 - - - +
120D LEU* 3.1 31.1 + - - +
134D LEU* 3.9 17.1 - - + +
0G ACE 5.6 1.8 + - - -
1G TRP 5.8 1.2 + - - +
3G TRP* 3.6 29.3 + - + -
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Residues in contact with LEU 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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169C LEU* 3.7 42.6 - - + +
170C LEU* 3.9 9.4 - - + +
173C ALA* 4.2 4.0 - - + -
113D LEU 3.1 4.5 + - - +
114D GLU* 3.7 7.6 - - - +
116D GLN* 1.3 81.2 - - - +
118D ALA* 1.3 64.4 + - - +
120D LEU* 3.3 3.2 + - - +
121D THR* 2.9 28.7 + - - +
127D LEU* 4.1 18.2 - - + -
130D ALA* 4.5 7.0 - - + -
131D LEU* 4.6 7.2 - - + -
134D LEU* 3.5 28.7 - - + -
3G TRP* 3.5 33.7 - - + -
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Residues in contact with ALA 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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169C LEU* 3.7 14.5 - - + +
114D GLU* 2.9 24.1 + - + +
115D ASN* 3.8 7.0 - - - +
117D LEU* 1.3 73.0 - - - +
119D PHE* 1.3 57.9 + - - +
121D THR* 2.8 20.5 + - - -
122D GLN* 2.9 37.8 + - - +
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Residues in contact with PHE 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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69D PRO* 3.4 39.3 - - + -
70D LEU 6.0 0.2 - - - -
71D GLU 5.4 5.2 - - - -
73D GLU 3.2 27.4 - - - -
75D TRP* 3.5 33.0 - - + -
78D PHE* 4.0 17.7 - + + -
115D ASN 2.9 18.8 + - - +
116D GLN 3.5 2.7 - - - +
117D LEU 3.2 0.2 - - - -
118D ALA* 1.3 76.4 - - - +
120D LEU* 1.3 69.2 + - + +
122D GLN* 3.1 17.7 + - + +
123D GLN* 3.1 43.3 + - + +
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Residues in contact with LEU 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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75D TRP* 3.6 28.9 - - + -
78D PHE* 5.2 1.3 - - + -
79D LEU* 4.1 19.1 - - + -
116D GLN 3.1 13.7 + - - +
117D LEU 3.9 2.7 - - - +
119D PHE* 1.3 87.6 - - + +
121D THR* 1.3 60.7 + - - +
123D GLN* 3.2 5.2 + - - +
124D GLY 3.2 6.6 + - - -
125D PHE* 3.1 45.0 + - + -
130D ALA* 4.0 17.7 - - + +
133D ALA* 5.3 3.6 - - + -
134D LEU* 3.5 45.8 - - + +
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Residues in contact with THR 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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169C LEU* 4.2 9.1 - - + +
117D LEU 2.9 16.6 + - - +
118D ALA* 2.8 23.9 + - - -
120D LEU* 1.3 74.4 - - - +
122D GLN* 1.3 63.6 + - - +
124D GLY* 3.1 12.1 + - - -
125D PHE 3.5 21.5 - - - +
127D LEU* 3.9 35.0 - - + +
130D ALA* 4.3 5.2 - - + -
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Residues in contact with GLN 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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118D ALA* 2.9 49.3 + - - +
119D PHE* 3.1 19.2 + - + +
121D THR* 1.3 77.4 + - - +
123D GLN* 1.3 64.3 + - + +
124D GLY* 3.1 5.5 + - - -
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Residues in contact with GLN 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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73D GLU 5.1 1.8 + - - -
74D SER* 4.3 4.5 - - - +
75D TRP* 3.1 44.2 + - + -
119D PHE* 3.1 43.0 + - + +
120D LEU* 3.2 12.1 + - - +
122D GLN* 1.3 80.2 - - + +
124D GLY* 1.3 58.0 + - - +
125D PHE* 3.7 1.8 - - + -
201D LEU* 4.8 10.2 - - - +
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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