Contacts of the helix formed by residues 160 - 170 (chain A) in PDB entry 1N8T
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 ASP 160 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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153A ASN* 4.2 5.6 + - - +
155A GLY* 3.4 21.9 - - - +
156A ILE 4.1 2.7 - - - -
157A GLY 3.0 7.6 + - - +
158A GLY 3.0 3.0 - - - -
159A SER* 1.3 81.9 - - - +
161A LEU* 1.3 68.9 + - - +
162A GLY 3.5 1.3 - - - -
163A PRO* 3.3 6.6 - - - +
164A LEU* 2.9 34.5 + - - +
182A PHE* 3.6 27.4 - - - +
183A VAL 4.4 1.6 + - - -
184A SER* 3.7 25.3 + - - -
385B ASN* 5.1 1.4 + - - -
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Residues in contact with LEU 161 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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157A GLY 3.0 14.4 + - - +
158A GLY* 5.2 0.7 - - - -
160A ASP* 1.3 80.8 - - - +
162A GLY* 1.3 57.4 + - - +
164A LEU* 3.2 15.8 + - + -
165A MET* 2.7 39.8 + - + +
346A ARG* 4.6 11.4 - - + +
349A ALA* 3.5 30.5 - - + +
350A TYR* 3.8 28.0 - - + +
353A GLN* 3.8 24.7 - - + +
389B ALA* 4.8 7.6 - - + -
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Residues in contact with GLY 162 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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158A GLY* 4.4 5.1 + - - -
161A LEU* 1.3 75.7 - - - +
163A PRO* 1.3 64.9 - - - +
165A MET* 3.7 0.3 - - - -
166A VAL* 2.8 39.2 + - - +
275A LEU* 3.7 15.0 - - - -
350A TYR* 3.3 28.3 - - - -
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Residues in contact with PRO 163 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153A ASN* 4.8 2.7 - - - +
158A GLY 3.9 10.1 - - - +
159A SER 4.0 7.9 - - - +
160A ASP 3.3 14.4 - - - +
162A GLY* 1.3 86.9 - - - +
164A LEU* 1.3 55.0 + - - +
167A THR* 2.7 37.6 + - - +
182A PHE* 3.5 11.8 - - + -
275A LEU* 4.5 7.9 - - + -
279A ILE* 3.6 31.2 - - + +
280A GLY* 4.8 1.6 - - - -
282A SER* 3.6 22.2 - - - +
283A ILE* 4.0 14.1 - - + +
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Residues in contact with LEU 164 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160A ASP* 2.9 26.5 + - - +
161A LEU* 3.6 11.2 - - + +
163A PRO* 1.3 74.9 - - - +
165A MET* 1.3 61.5 + - - +
167A THR* 3.2 2.0 + - - -
168A GLU* 3.0 45.3 + - + +
182A PHE* 3.5 44.2 - - + +
345A HIS* 5.7 0.4 - - + -
346A ARG* 3.6 36.6 - - + -
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Residues in contact with MET 165 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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161A LEU* 2.7 21.6 + - + +
162A GLY 3.8 0.4 - - - +
164A LEU* 1.3 79.7 - - - +
166A VAL* 1.3 69.5 + - + +
168A GLU* 3.3 3.2 + - - +
169A ALA* 2.9 36.2 + - - +
275A LEU* 5.1 0.2 - - + -
343A TYR 4.9 0.5 - - - +
344A LEU* 4.9 1.6 - - + -
346A ARG* 3.4 40.8 - - + +
347A PHE* 3.7 27.1 - - + +
350A TYR* 3.6 38.8 - - + -
486A LEU* 4.7 4.5 - - - -
490A ILE* 4.2 21.1 - - + -
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Residues in contact with VAL 166 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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162A GLY 2.8 24.5 + - - +
165A MET* 1.3 81.8 - - + +
167A THR* 1.3 55.8 + - - +
169A ALA* 3.1 4.8 + - - +
170A LEU* 2.8 52.4 + - + +
275A LEU* 3.9 25.4 - - + -
283A ILE* 3.7 31.4 - - + -
295A LEU* 4.3 7.2 - - + -
486A LEU* 4.0 5.8 - - + -
490A ILE* 4.2 16.2 - - + -
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Residues in contact with THR 167 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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163A PRO 2.7 25.5 + - - +
164A LEU 3.2 5.2 + - - -
166A VAL* 1.3 72.8 - - - +
168A GLU* 1.3 65.7 + - - +
170A LEU* 3.7 4.5 - - - +
171A LYS* 3.2 30.5 + - - +
180A VAL* 3.9 16.6 - - + +
182A PHE* 3.1 21.7 - - + -
282A SER 4.1 2.5 - - - +
283A ILE* 3.9 23.1 - - + +
286A HIS* 3.8 32.3 + - + +
287A VAL* 5.5 1.8 - - + -
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Residues in contact with GLU 168 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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164A LEU* 3.0 37.7 + - + +
165A MET* 3.7 6.5 - - - +
167A THR* 1.3 78.6 + - - +
169A ALA* 1.3 61.5 + - - +
170A LEU 3.5 0.3 + - - -
171A LYS* 3.7 26.3 + - - +
182A PHE* 5.9 2.6 - - + -
343A TYR* 3.3 32.0 - - - +
345A HIS* 2.8 38.0 + - + +
346A ARG* 4.8 2.2 - - + +
193B LYS* 4.9 7.4 + - - -
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Residues in contact with ALA 169 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165A MET* 2.9 19.8 + - - +
166A VAL 3.1 4.7 + - - +
168A GLU* 1.3 78.4 - - - +
170A LEU* 1.3 62.7 + - + +
171A LYS 3.4 2.4 + - - -
172A PRO* 4.3 2.9 - - - +
173A TYR* 5.4 0.5 - - - -
343A TYR* 3.4 26.1 + - - +
344A LEU* 3.8 27.8 - - + -
412A GLN* 6.0 0.5 - - - +
481A LEU* 4.2 10.1 - - + +
486A LEU* 3.9 18.8 - - + -
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Residues in contact with LEU 170 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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166A VAL* 2.8 39.1 + - + +
167A THR* 3.7 3.6 - - - +
169A ALA* 1.3 85.3 - - + +
171A LYS* 1.3 65.7 + - - +
172A PRO* 3.3 5.4 - - - -
173A TYR* 2.8 24.3 + - + +
283A ILE* 5.1 1.6 - - + -
287A VAL* 3.5 29.2 - - + +
295A LEU* 4.6 4.5 - - + -
481A LEU* 4.4 8.3 - - + +
482A THR 4.3 4.9 - - - +
483A PRO* 4.1 43.1 - - + -
486A LEU* 3.6 22.7 - - + -
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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