Contacts of the helix formed by residues 164 - 170 (chain P) in PDB entry 6NR8
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 LEU 164 (chain P).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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160P VAL* 2.7 43.3 + - + +
161P SER* 4.1 3.1 - - - -
163P LEU* 1.3 71.5 - - + +
165P ARG* 1.3 61.4 + - - +
166P THR 3.5 0.4 - - - -
167P SER* 3.7 12.2 - - - +
168P ILE* 3.3 25.8 + - - +
180P ALA* 4.7 1.7 - - - +
183P ILE* 3.8 45.8 - - + +
184P ALA 4.5 0.2 - - - +
187P CYS* 4.7 4.7 - - - -
395P GLY* 3.7 21.1 - - - +
398P THR* 3.7 34.5 - - + -
399P PHE* 4.7 4.0 - - + +
402P LEU* 6.5 0.2 - - + -
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Residues in contact with ARG 165 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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161P SER* 3.2 31.0 + - - +
162P SER* 3.5 15.4 + - - +
163P LEU 3.1 1.0 - - - -
164P LEU* 1.3 77.6 - - - +
166P THR* 1.3 52.0 + - - +
168P ILE* 3.1 10.6 + - - +
169P MET* 2.6 57.1 + - + +
176P GLU* 3.5 14.8 - - + +
177P VAL* 3.3 52.3 + - - +
180P ALA* 4.2 7.2 - - + +
181P LYS* 5.7 2.6 - - - +
496P GLY* 4.9 8.1 - - - +
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Residues in contact with THR 166 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49P PRO* 5.7 2.4 - - - +
163P LEU 3.4 16.8 - - - +
165P ARG* 1.3 76.1 - - - +
167P SER* 1.3 69.0 + - - +
168P ILE 3.3 0.2 - - - -
169P MET* 3.7 14.0 - - - +
170P SER* 3.3 21.0 + - - -
496P GLY 3.7 11.8 + - - +
497P ILE* 3.4 25.7 - - - +
498P LEU* 3.3 40.8 + - + +
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Residues in contact with SER 167 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99P ASP* 4.1 7.3 - - - +
163P LEU 4.0 6.2 + - - -
164P LEU* 3.6 31.5 + - - +
165P ARG 3.2 0.4 - - - -
166P THR* 1.3 82.2 - - - +
168P ILE* 1.3 62.0 + - - +
170P SER* 2.7 23.2 + - - -
171P LYS* 4.2 6.9 + - - +
391P ALA* 4.6 5.5 - - - +
394P ASP* 5.2 5.5 - - - +
395P GLY* 4.8 7.4 - - - -
398P THR* 3.8 18.6 + - - +
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Residues in contact with ILE 168 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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164P LEU 3.3 12.5 + - - +
165P ARG 3.2 11.7 - - - +
167P SER* 1.3 76.0 - - - +
169P MET* 1.3 64.8 + - - +
170P SER 3.3 0.7 - - - -
171P LYS 3.7 1.1 + - - -
172P GLN* 3.2 35.3 + - - +
176P GLU* 3.2 21.0 - - - +
179P LEU* 3.7 17.7 - - + +
180P ALA* 3.4 34.3 - - + +
183P ILE* 4.4 18.6 - - + -
391P ALA* 3.7 36.6 - - + +
392P VAL* 5.1 2.9 - - + -
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Residues in contact with MET 169 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49P PRO* 2.8 35.4 - - + +
50P ASN* 3.6 9.8 + - - +
165P ARG* 2.6 39.3 + - + +
166P THR* 3.7 21.3 - - - +
168P ILE* 1.3 73.9 - - - +
170P SER* 1.3 58.7 - - - +
172P GLN 3.0 21.8 - - - +
176P GLU* 3.1 27.8 + - + +
496P GLY 5.1 2.7 - - - +
497P ILE* 3.9 33.2 - - + -
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Residues in contact with SER 170 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46P ALA 4.4 5.7 - - - +
47P TYR* 3.6 17.9 - - - -
48P GLY 3.3 23.7 - - - +
49P PRO 4.1 0.7 - - - -
51P GLY 4.2 12.2 + - - -
67P ASN* 4.5 0.5 - - - +
99P ASP* 2.5 29.8 + - - -
166P THR 3.3 10.2 + - - -
167P SER 2.7 19.8 + - - -
169P MET* 1.3 78.1 - - - +
171P LYS* 1.3 68.7 + - - +
172P GLN 3.7 0.2 - - - -
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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