Contacts of the helix formed by residues 115 - 124 (chain D) in PDB entry 1SHZ
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 115 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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110D TRP* 3.1 24.7 - - + +
112D ASP* 2.7 24.7 + - - +
114D LYS* 1.3 75.4 + - - +
116D GLN* 1.3 54.2 + - - -
117D LEU 3.1 1.3 - - - -
118D HIS* 2.7 54.9 + - - +
119D GLY 3.0 10.6 + - - -
151D ALA* 3.8 14.2 + - - +
152D LEU* 4.0 9.0 - - + -
155D ASP* 3.0 36.3 + - - +
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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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148C VAL 5.0 1.1 - - - +
151C GLY 3.9 9.5 + - - -
152C ARG* 3.4 41.9 - - + +
155C GLU* 3.4 28.7 - - - +
158C ARG* 4.8 0.2 - - - +
103D ARG* 4.4 0.2 + - - -
110D TRP* 3.1 40.0 - - + -
113D ASN 3.3 13.6 + - - +
114D LYS 2.9 1.8 + - - +
115D ASN* 1.3 77.8 - - - +
117D LEU* 1.3 68.5 + - + +
119D GLY 3.6 0.3 + - - -
120D ASP* 2.9 59.6 + - - +
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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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144C GLN 5.7 0.7 - - - +
147C GLN* 4.0 26.2 - - + +
148C VAL* 3.5 44.4 - - + +
151C GLY* 5.8 2.5 - - - -
114D LYS 3.8 9.9 - - - +
115D ASN 3.1 0.8 - - - -
116D GLN* 1.3 81.4 - - + +
118D HIS* 1.3 63.1 + - + +
120D ASP* 3.8 5.0 - - - +
121D LYS* 3.0 27.9 + - - +
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Residues in contact with HIS 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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114D LYS* 3.8 21.3 + - - -
115D ASN* 2.7 48.6 + - - +
117D LEU* 1.3 71.8 - - + +
119D GLY* 1.3 59.1 + - - +
120D ASP 2.9 1.1 - - - -
121D LYS* 2.7 26.7 + - - +
122D LEU* 2.9 14.6 + - - +
147D PRO* 4.8 4.7 - - + -
148D ALA* 3.7 29.6 - - + +
151D ALA* 3.8 16.1 - - + +
152D LEU* 3.7 19.3 - - + -
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Residues in contact with GLY 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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100D VAL* 4.1 13.5 - - - +
110D TRP* 4.3 12.1 - - - -
115D ASN 3.0 8.2 + - - -
116D GLN 4.1 1.6 - - - -
118D HIS* 1.3 80.0 - - - +
120D ASP* 1.3 57.3 + - - +
122D LEU* 3.8 1.8 + - - +
123D MET* 3.0 35.5 + - - +
152D LEU* 3.9 19.0 - - - +
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Residues in contact with ASP 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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47C GLN* 4.2 16.2 - - - +
151C GLY* 4.2 10.6 - - - +
158C ARG* 3.5 32.9 + - - -
116D GLN* 2.9 39.9 + - - +
117D LEU* 3.8 6.3 - - - +
118D HIS 2.9 1.0 - - - -
119D GLY* 1.3 79.2 - - - +
121D LYS* 1.3 61.9 + - - +
123D MET* 3.9 7.2 - - - +
124D ALA* 3.4 19.2 + - - +
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Residues in contact with LYS 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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117D LEU 3.0 16.6 + - - +
118D HIS* 2.7 17.5 + - - +
120D ASP* 1.3 71.4 - - - +
122D LEU* 1.3 63.5 + - - +
124D ALA* 3.2 19.3 + - + +
144D GLN* 3.3 29.0 + - - +
145D TYR* 3.7 33.9 + - + +
148D ALA* 4.6 16.6 - - + -
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Residues in contact with LEU 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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93D ILE* 4.4 21.1 - - + +
96D MET* 3.4 20.2 - - + -
97D ARG* 3.1 19.8 - - + -
100D VAL* 4.9 4.5 - - + -
118D HIS 2.9 8.7 + - - +
119D GLY* 4.1 4.9 - - - +
121D LYS* 1.3 80.3 - - - +
123D MET* 1.3 55.8 + - + +
125D PHE* 3.0 28.4 - - - +
145D TYR* 3.7 26.2 - - + -
148D ALA* 4.3 9.9 - - + -
149D ILE* 3.7 26.5 - - + -
152D LEU* 3.3 31.9 - - + -
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Residues in contact with MET 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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47C GLN* 4.5 17.6 - - - +
158C ARG* 5.9 1.3 - - - +
97D ARG* 3.0 43.7 + - - +
100D VAL* 3.1 23.1 - - + -
101D ASP* 3.2 47.1 - - + +
104D GLU* 5.8 3.1 - - - +
119D GLY 3.0 24.1 + - - +
120D ASP* 4.1 9.9 - - - +
121D LYS 3.3 0.6 - - - -
122D LEU* 1.3 75.9 - - - +
124D ALA* 1.3 56.7 + - - +
125D PHE 3.0 3.4 + - - +
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Residues in contact with ALA 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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120D ASP 3.4 12.7 + - - +
121D LYS* 3.2 15.0 + - - +
122D LEU 3.1 1.0 - - - -
123D MET* 1.3 75.8 - - - +
125D PHE* 1.3 62.5 + - - +
126D ASP* 3.2 5.0 + - - +
145D TYR* 4.8 3.8 + - - +
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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