Contacts of the helix formed by residues 165 - 169 (chain K) 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 PHE 165 (chain K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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127G THR* 3.2 45.0 + - - +
130G GLU* 4.7 8.3 - - - -
155G ASN* 5.6 2.0 - - - -
187G TYR* 5.7 0.2 - - - +
141K LEU* 4.2 13.9 - - + -
145K GLN* 3.7 51.1 - - + +
148K ALA* 4.1 17.9 - - + -
149K VAL* 3.9 7.9 - - + -
161K LYS* 3.2 35.7 - - + -
162K LEU* 3.4 9.5 + - - +
163K PHE 3.2 0.4 - - - -
164K SER* 1.3 80.7 - - - +
166K THR* 1.3 62.2 + - - +
167K PRO* 3.5 2.2 - - - -
168K ALA 3.5 2.4 + - - -
169K TRP* 3.2 28.9 + - + +
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Residues in contact with THR 166 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115K ILE* 5.4 1.7 - - - +
116K ASP* 4.0 16.8 + - - -
162K LEU 3.7 3.1 + - - -
163K PHE* 3.2 33.2 + - - +
165K PHE* 1.3 73.8 - - - +
167K PRO* 1.4 69.3 - - - +
168K ALA 3.1 2.7 - - - -
169K TRP* 3.1 44.0 + - - +
174K LYS* 4.5 8.1 + - - +
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Residues in contact with PRO 167 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124G ALA 3.9 16.8 - - - +
125G ARG* 2.8 38.0 + - + +
127G THR* 4.4 4.9 - - + -
137H TYR* 4.9 4.9 - - - +
143H ASP* 2.5 33.2 - - + +
147H GLN* 5.4 0.4 - - - +
163K PHE 3.4 14.4 - - - +
164K SER 3.9 8.1 - - - +
165K PHE 3.8 3.1 - - - -
166K THR* 1.4 91.3 - - - +
168K ALA* 1.3 57.6 + - - +
169K TRP 3.2 1.8 + - - +
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Residues in contact with ALA 168 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125G ARG 2.7 24.0 + - - +
127G THR* 3.1 27.4 - - - +
185G GLN* 3.1 20.9 - - - +
187G TYR* 2.4 31.7 - - - +
188G LEU* 3.7 15.3 - - + +
165K PHE 3.5 4.9 + - - +
166K THR 3.1 1.6 - - - -
167K PRO* 1.3 76.4 - - - +
169K TRP* 1.3 53.1 + - - +
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Residues in contact with TRP 169 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125G ARG* 2.9 17.4 + - - -
187G TYR* 2.7 31.8 + + - -
115K ILE* 5.6 5.2 - - + -
136K LEU* 4.8 6.3 - - + -
140K VAL* 2.7 34.4 - - + +
141K LEU* 4.4 15.5 - - + -
145K GLN* 5.2 0.6 + - - -
162K LEU* 4.3 23.1 - - + -
163K PHE* 6.3 0.4 - + - -
165K PHE* 3.2 22.0 + - + +
166K THR* 3.1 31.2 + - - +
167K PRO 4.1 0.9 - - - +
168K ALA* 1.3 80.2 - - - +
170K ASN* 1.3 59.7 + - - +
173K CYS* 3.6 15.5 - - - -
174K LYS* 3.7 36.9 + - + -
177K LEU* 3.6 37.0 - - + -
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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