Contacts of the helix formed by residues 154 - 159 (chain B) in PDB entry 6U37
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 154 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70B TYR 5.6 0.9 - - - -
71B GLN* 6.4 0.4 - - - -
123B PHE 2.7 19.1 + - - -
124B TYR* 3.6 8.2 - - - +
153B VAL* 1.3 73.8 - - - +
155B ALA* 1.3 59.0 + - - -
156B PHE* 5.3 0.7 - - - -
157B GLY 3.2 0.5 + - - -
158B PHE* 2.9 26.2 + - - +
285B GLU* 3.5 19.5 - - - -
299B PHE* 3.5 17.1 - - - +
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Residues in contact with ALA 155 (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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47B PHE* 3.4 13.1 - - + -
153B VAL 3.7 0.2 + - - -
154B GLY* 1.3 72.8 - - - -
156B PHE* 1.3 69.6 + - + +
158B PHE 3.5 0.2 + - - -
159B LEU* 3.0 37.5 + - + +
251B LEU* 3.8 19.5 - - + -
281B LEU* 5.1 10.3 - - + +
285B GLU* 4.0 4.9 + - + +
299B PHE* 3.6 29.3 - - + -
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Residues in contact with PHE 156 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46B ARG* 3.9 20.0 - - + -
47B PHE* 4.2 13.5 + + - -
69B CYS* 6.5 0.9 - - + -
70B TYR* 3.6 25.6 - - + -
94B GLU* 3.5 30.1 - - + +
152B ARG* 3.5 32.2 + - + -
153B VAL 3.8 7.6 - - - +
154B GLY* 3.2 0.6 - - - -
155B ALA* 1.3 81.5 - - + +
157B GLY* 1.3 57.0 + - - +
171B VAL* 3.6 9.4 - - - +
278B ALA* 3.3 42.6 - - + -
281B LEU* 4.1 18.2 - - + -
282B VAL* 3.6 23.6 - - + -
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Residues in contact with GLY 157 (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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152B ARG* 3.4 28.9 - - - -
153B VAL 3.4 3.2 + - - -
154B GLY 3.2 4.3 + - - -
155B ALA 3.1 0.4 - - - -
156B PHE* 1.3 81.6 - - - +
158B PHE* 1.3 67.7 + - - +
159B LEU 4.0 0.7 - - - -
171B VAL* 3.2 18.1 + - - +
172B GLY 2.9 21.4 + - - -
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Residues in contact with PHE 158 (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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123B PHE* 3.5 48.9 - + + -
151B TYR* 4.6 6.5 - + - -
152B ARG 3.4 18.6 - - - -
153B VAL* 4.3 1.1 - - - -
154B GLY 2.9 8.1 + - - +
157B GLY* 1.3 88.6 - - - +
159B LEU* 1.3 65.1 + - - +
160B ALA* 3.3 9.9 + - - +
169B GLY* 4.9 0.8 - - - -
170B ASN* 4.1 13.9 + - - +
172B GLY* 3.8 14.4 - - - -
173B LEU* 3.9 22.0 - - + -
244B ALA* 5.9 0.7 - - - +
299B PHE* 3.5 32.2 - - - +
300B VAL 3.7 12.3 - - - +
301B PRO* 3.7 35.0 - - + -
302B VAL* 5.6 0.5 - - - +
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Residues in contact with LEU 159 (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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47B PHE* 4.0 21.4 - - + +
155B ALA* 3.0 29.8 + - + +
157B GLY 5.5 0.2 - - - -
158B PHE* 1.3 76.5 - - - +
160B ALA* 1.3 62.7 + - - +
161B LEU* 5.0 3.4 - - + +
167B ALA* 3.9 26.4 - - + +
169B GLY* 3.8 12.1 + - - -
171B VAL* 5.9 1.2 - - - +
248B ALA* 3.8 25.1 - - + -
251B LEU* 3.7 29.6 - - + -
270B VAL* 5.3 0.7 - - + -
273B LEU* 4.1 22.7 - - + -
299B PHE* 3.7 19.3 - - + -
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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