Contacts of the helix formed by residues 151 - 156 (chain A) in PDB entry 6TT0
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 GLY 151 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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68A GLN 5.6 0.4 - - - -
69A GLN* 6.3 0.4 - - - -
120A PHE 2.7 17.6 + - - -
121A TYR* 3.6 14.8 - - - +
150A VAL* 1.3 72.4 - - - +
152A ALA* 1.3 66.2 + - - -
153A PHE* 4.9 2.7 - - - -
155A PHE* 3.2 15.5 + - - +
278A GLU* 4.2 13.2 - - - -
292A PHE* 3.1 23.7 - - - +
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Residues in contact with ALA 152 (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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45A PHE* 3.5 8.7 - - + -
151A GLY* 1.3 71.9 - - - -
153A PHE* 1.3 69.2 + - + +
156A LEU* 3.1 28.7 + - + +
248A LEU* 4.1 8.5 - - + -
274A LEU* 4.1 30.7 - - + +
278A GLU* 4.4 5.6 + - + +
292A PHE* 3.8 34.1 - - + -
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Residues in contact with PHE 153 (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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44A ARG* 4.3 18.4 - - + -
45A PHE* 4.3 17.0 + + - -
68A GLN* 3.7 28.7 - - + -
92A GLU* 3.6 29.6 - - + +
149A ARG* 3.6 31.8 + - + -
150A VAL 3.5 13.9 - - - +
151A GLY* 4.9 1.3 - - - -
152A ALA* 1.3 83.9 - - + +
154A GLY* 1.3 56.7 + - - +
168A VAL* 3.8 9.5 - - - +
271A PRO* 3.7 44.6 - - + -
274A LEU* 4.5 15.9 - - + -
275A ILE* 4.0 15.3 - - + -
278A GLU* 5.9 1.1 - - - -
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Residues in contact with GLY 154 (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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149A ARG* 3.3 28.2 - - - +
150A VAL 3.3 7.1 + - - -
152A ALA 3.2 0.4 - - - -
153A PHE* 1.3 79.3 - - - +
155A PHE* 1.3 68.3 + - - +
156A LEU 3.9 0.4 - - - -
168A VAL* 3.2 19.6 + - - +
169A GLY 2.9 22.0 + - - -
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Residues in contact with PHE 155 (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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120A PHE* 3.6 38.1 - + + -
148A TYR* 4.6 6.3 - + - -
149A ARG 3.4 18.4 - - - -
150A VAL* 4.4 0.4 - - - -
151A GLY 3.2 10.2 + - - +
154A GLY* 1.3 96.4 - - - +
156A LEU* 1.3 68.2 + - - +
157A ALA* 3.4 8.0 + - - +
166A GLY* 4.9 1.4 - - - -
167A ASN* 4.1 13.4 + - - +
169A GLY* 3.8 17.0 - - - -
170A LEU* 4.0 19.5 - - + -
292A PHE* 3.4 43.5 - - - +
293A VAL 3.6 12.9 - - - +
294A PRO* 3.6 34.3 - - + -
295A VAL* 5.5 0.2 - - - +
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Residues in contact with LEU 156 (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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45A PHE* 3.8 29.3 - - + +
152A ALA* 3.1 21.5 + - + +
154A GLY 3.9 0.4 - - - -
155A PHE* 1.3 76.8 - - - +
157A ALA* 1.4 58.8 + - - +
158A LEU* 4.0 11.0 - - + -
164A ALA* 3.7 24.3 - - + +
166A GLY* 3.3 17.7 + - - -
168A VAL* 5.9 1.6 - - - +
245A ALA* 3.7 26.5 - - + -
248A LEU* 3.9 18.4 - - + -
263A ILE* 5.3 1.8 - - + -
266A LEU* 4.0 19.1 - - + -
292A PHE* 3.7 24.7 - - + -
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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