Contacts of the helix formed by residues 174 - 179 (chain B) in PDB entry 6D6U
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 GLU 174 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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173B ARG* 1.3 75.1 - - + +
175B PRO* 1.3 68.3 - - + +
176B ALA* 3.1 3.5 - - + +
177B ARG* 2.8 39.7 + - + +
178B SER 3.2 6.2 + - - -
92I TYR 4.8 3.4 - - - +
93I SER* 4.4 7.2 + - - +
94I TYR* 3.2 55.7 + - - -
95I PRO* 5.1 2.2 - - - +
35J TYR* 4.8 5.1 + - - +
47J TRP* 5.5 0.3 - - - -
50J ARG* 2.4 45.7 + - - +
103J TRP* 3.9 11.5 - - + -
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Residues in contact with PRO 175 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171B TRP* 4.3 13.2 - - + -
173B ARG 3.2 5.1 - - - +
174B GLU* 1.3 81.7 - - + +
176B ALA* 1.3 60.1 + - - +
177B ARG 3.2 0.6 + - - -
178B SER* 3.6 17.8 + - - +
179B VAL 4.8 0.3 + - - -
198B VAL* 3.2 39.3 - - + +
32I TYR* 4.4 22.2 - - + -
91I SER 3.7 23.6 - - - +
92I TYR* 3.7 9.9 - - + +
103J TRP* 4.1 26.9 - - + +
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Residues in contact with ALA 176 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174B GLU* 2.9 2.8 + - + +
175B PRO* 1.3 76.5 - - - +
177B ARG* 1.3 65.1 + - + +
178B SER 3.5 0.2 - - - -
179B VAL 5.1 4.9 + - - +
198B VAL* 4.9 0.2 - - - -
92I TYR* 3.1 48.9 + - + +
93I SER* 4.3 13.5 - - - +
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Residues in contact with ARG 177 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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173B ARG* 3.8 31.0 + - + +
174B GLU* 2.8 30.4 + - + +
176B ALA* 1.3 84.6 - - + +
178B SER* 1.3 64.8 + - - +
179B VAL 3.6 2.5 - - - -
180B VAL* 3.3 17.2 - - + +
94I TYR* 3.3 27.0 + - - -
50J ARG* 4.9 2.2 - - - +
59J LYS* 4.1 21.0 - - - +
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Residues in contact with SER 178 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43B THR 5.2 0.7 - - - -
44B ASP* 2.8 27.7 - - - +
45B ILE 3.2 1.1 - - - +
171B TRP* 3.3 47.6 - - - +
172B THR 4.3 0.2 + - - -
173B ARG* 3.5 16.5 + - - +
174B GLU 3.2 10.7 + - - -
175B PRO* 3.8 8.5 - - - +
176B ALA 3.5 2.2 - - - -
177B ARG* 1.3 79.8 - - - +
179B VAL* 1.3 61.2 + - - +
180B VAL* 2.9 14.0 + - - +
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Residues in contact with VAL 179 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45B ILE* 3.8 25.8 - - + -
47B VAL* 4.7 1.8 - - + -
171B TRP* 4.0 17.0 - - + -
175B PRO 4.8 1.8 + - - -
176B ALA 5.1 4.5 + - - +
177B ARG 4.6 2.1 - - - -
178B SER* 1.3 71.3 - - - +
180B VAL* 1.3 64.0 + - - +
181B VAL* 4.1 0.9 + - + -
196B GLN* 4.0 36.7 - - + +
198B VAL* 3.8 27.4 - - + -
215B THR* 4.0 17.9 - - + +
217B PHE* 4.2 18.4 - - + -
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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
------------------------------------------------------------
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