Contacts of the helix formed by residues 142 - 150 (chain I) in PDB entry 6N1H
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 THR 142 (chain I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128E ASN* 3.8 21.1 + - - +
131E TRP* 6.5 0.4 - - + -
183E GLU 5.6 1.1 - - - +
184E SER* 4.0 18.8 - - - +
137I TYR* 4.2 2.7 - - - -
138I GLY* 6.0 0.2 - - - -
140I VAL 3.4 7.5 + - - +
141I LEU* 1.3 75.1 - - - +
143I ASP* 1.3 54.9 + - - +
144I GLU* 3.7 13.9 + - - +
145I GLN* 3.0 28.8 + - - +
146I TYR* 2.6 34.1 + - - +
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Residues in contact with ASP 143 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124H ALA* 4.6 5.4 - - + +
156H PRO* 5.2 1.8 - - + -
137I TYR* 3.7 24.9 + - - +
142I THR* 1.3 74.7 - - - +
144I GLU* 1.3 66.3 + - - +
146I TYR* 4.0 12.5 - - - -
147I GLN* 3.2 49.2 + - - +
119L ARG* 5.5 0.5 + - - -
163L PHE 6.0 0.2 - - - -
164L SER* 6.1 0.5 - - - -
167L PRO* 2.5 40.7 - - + +
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Residues in contact with GLU 144 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128E ASN* 4.9 6.5 - - - +
130E GLU* 4.7 15.0 - - + +
131E TRP* 3.8 22.6 + - + -
124H ALA* 2.8 36.2 - - - +
154H THR* 4.3 5.4 - - - +
156H PRO* 3.7 30.1 - - + -
160H ARG* 4.3 15.4 + - - +
142I THR* 3.8 17.3 + - - +
143I ASP* 1.3 86.6 + - - +
145I GLN* 1.3 59.3 + - - +
147I GLN* 5.1 0.2 - - - -
148I ALA* 3.5 21.3 + - - +
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Residues in contact with GLN 145 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127E THR* 3.7 7.5 + - - +
128E ASN* 3.5 37.1 - - - +
130E GLU* 5.1 1.6 - - - +
185E GLN* 4.3 4.8 + - - -
187E TYR* 4.9 5.0 + - - -
140I VAL* 3.7 8.6 - - - +
141I LEU* 3.4 35.5 - - + +
142I THR* 3.0 22.1 + - - +
144I GLU* 1.3 78.8 - - - +
146I TYR* 1.3 63.6 + - - +
147I GLN 3.4 0.2 - - - -
148I ALA 3.5 0.6 + - - -
149I VAL* 3.3 27.4 + - - +
165I PHE* 3.7 44.6 - - + +
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Residues in contact with TYR 146 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133I LEU* 3.5 40.9 - - + +
134I ASP* 2.9 23.0 + - - -
137I TYR* 3.7 27.4 - + + -
141I LEU* 4.6 8.5 - - + +
142I THR 2.6 20.2 + - - +
143I ASP* 3.9 15.3 - - - +
144I GLU 3.4 0.2 - - - -
145I GLN* 1.3 74.3 - - - +
147I GLN* 1.3 65.5 + - + +
149I VAL* 3.5 13.3 + - - +
150I ARG* 3.5 51.5 + - - +
119L ARG* 3.3 28.9 + - - -
160L ARG* 3.6 11.1 + - - -
164L SER* 6.4 1.8 - - - -
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Residues in contact with GLN 147 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124H ALA 5.9 1.0 + - - -
127H THR* 5.3 3.2 - - - +
153H PRO 4.6 2.8 - - - +
154H THR* 3.0 23.4 + - - +
155H ASN* 3.0 21.6 + - - +
156H PRO* 2.3 40.1 - - + +
143I ASP* 3.2 35.7 + - - +
144I GLU 4.6 0.7 - - - +
146I TYR* 1.3 83.4 - - + +
148I ALA* 1.3 64.0 + - - +
149I VAL 3.5 0.2 + - - -
150I ARG* 3.5 21.4 + - - +
151I ALA* 4.9 0.9 - - - +
164L SER* 4.3 25.9 + - - +
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Residues in contact with ALA 148 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130E GLU* 5.7 2.5 - - - +
154H THR* 2.5 24.9 - - + +
144I GLU 3.5 14.5 + - - +
145I GLN 3.9 5.4 - - - +
146I TYR 3.3 1.0 - - - -
147I GLN* 1.3 77.5 - - - +
149I VAL* 1.3 62.7 + - - +
151I ALA* 4.3 4.9 + - - +
152I GLU* 4.1 6.8 - - - +
161I LYS* 3.4 24.2 - - + +
165I PHE* 4.1 17.0 - - + -
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Residues in contact with VAL 149 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129I VAL* 4.5 1.8 - - + -
133I LEU* 3.7 36.1 - - + -
141I LEU* 5.2 3.4 - - + -
145I GLN 3.3 16.4 - - - +
146I TYR 3.5 7.3 + - - +
147I GLN 3.2 0.4 - - - -
148I ALA* 1.3 77.0 - - - +
150I ARG* 1.3 52.3 + - - +
151I ALA 2.7 28.1 + - - +
152I GLU* 4.5 0.9 - - - +
158I LYS* 3.3 40.8 - - + +
161I LYS* 3.7 24.9 - - + +
162I LEU* 4.3 5.6 - - + +
165I PHE* 3.9 10.3 - - + -
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Residues in contact with ARG 150 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153H PRO* 5.3 3.6 - - - +
130I GLU* 5.8 4.6 - - + +
133I LEU* 3.7 17.9 - - + -
146I TYR* 3.5 55.6 + - - +
147I GLN* 3.5 13.0 + - - +
148I ALA 3.4 1.0 - - - -
149I VAL* 1.3 71.3 - - - +
151I ALA* 1.3 60.4 + - - +
158I LYS* 4.5 16.1 - - - +
157L SER* 4.4 9.7 + - - -
160L ARG* 3.5 48.5 + - - +
161L LYS* 4.9 8.2 - - - +
164L SER* 5.2 4.6 - - - -
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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