Contacts of the helix formed by residues 162 - 174 (chain D) in PDB entry 2FG8
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 162 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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162B GLU* 3.0 34.2 + - + +
165B LEU* 5.4 4.2 - - + +
160C GLY 3.7 18.5 - - - +
161C PRO* 3.7 9.9 - - - +
162C GLU* 3.0 37.8 + - + +
158D LEU 4.4 0.7 - - - +
159D GLY 4.4 3.6 - - - -
160D GLY* 3.3 2.7 - - - -
161D PRO* 1.3 92.7 - - + +
163D ALA* 1.3 58.1 + - - +
164D GLY 3.1 3.1 - - - +
165D LEU* 3.3 24.4 + - + +
166D GLY* 2.9 24.1 + - - -
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Residues in contact with ALA 163 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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158D LEU 3.5 14.7 - - - +
159D GLY* 3.9 2.7 - - - -
160D GLY* 3.3 26.1 - - - +
161D PRO 3.4 2.6 + - - -
162D GLU* 1.3 75.1 - - - +
164D GLY* 1.3 59.8 + - - +
165D LEU 3.4 0.2 - - - -
166D GLY 3.5 0.8 - - - -
167D GLU* 2.8 30.7 + - - +
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Residues in contact with GLY 164 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157C ARG* 3.5 39.0 - - - +
161D PRO 5.2 0.2 + - - -
162D GLU* 3.1 1.4 - - - +
163D ALA* 1.3 76.9 - - - +
165D LEU* 1.3 63.6 + - - +
167D GLU* 3.3 5.4 + - - -
168D TYR* 3.2 18.0 + - - +
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Residues in contact with LEU 165 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165B LEU* 4.6 14.6 - - + -
157C ARG 4.1 3.0 + - - -
158C LEU* 4.0 29.8 - - + -
162C GLU* 4.6 4.0 - - + -
165C LEU* 3.5 31.9 - - + -
166C GLY* 4.8 4.0 - - - +
169C LEU* 3.4 29.8 - - + -
162D GLU* 3.3 31.7 + - + +
164D GLY* 1.3 74.9 - - - +
166D GLY* 1.3 64.1 + - - +
168D TYR* 3.5 1.7 + - + +
169D LEU* 3.1 29.9 + - + +
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Residues in contact with GLY 166 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165B LEU* 5.1 1.8 - - - -
155D LEU* 5.9 0.7 - - - -
158D LEU* 3.7 38.1 - - - +
162D GLU 2.9 14.4 + - - -
163D ALA 3.3 3.8 + - - -
164D GLY 3.1 0.2 - - - -
165D LEU* 1.3 78.8 - - - +
167D GLU* 1.3 61.1 + - - +
169D LEU* 3.2 5.0 + - - +
170D PHE* 3.1 23.2 + - - +
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Residues in contact with GLU 167 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157C ARG* 3.6 19.0 + - - +
48D LEU* 3.7 19.4 - - + +
95D LYS* 3.5 23.8 - - - +
96D THR* 2.6 52.7 + - + +
97D PRO* 4.6 5.4 - - + -
155D LEU* 5.1 5.6 - - + -
163D ALA 2.8 19.7 + - - +
164D GLY* 3.3 7.4 + - - +
166D GLY* 1.3 72.9 - - - +
168D TYR* 1.3 60.2 + - - +
170D PHE* 3.7 5.8 + - - +
171D GLU* 3.4 21.3 + - - +
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Residues in contact with TYR 168 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154C ASN* 3.7 24.0 - - + -
157C ARG* 4.4 7.4 - - - +
158C LEU* 3.4 37.0 - - + -
169C LEU* 3.2 33.4 + - + -
170C PHE* 3.4 18.8 - + - -
173C LEU* 3.4 15.8 - - + +
174C THR* 2.6 29.7 + - - -
48D LEU* 4.8 5.6 - - + -
164D GLY 3.2 7.0 + - - +
165D LEU* 3.8 3.6 - - + +
166D GLY 3.2 0.8 - - - -
167D GLU* 1.3 74.3 - - - +
169D LEU* 1.3 76.0 + - + +
171D GLU* 3.5 6.0 + - - +
172D ARG* 3.0 51.4 + - + +
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Residues in contact with LEU 169 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165B LEU* 3.3 33.7 - - + -
168B TYR* 4.0 13.7 - - + -
169B LEU* 3.8 24.7 - - + -
169C LEU* 3.8 24.2 - - + -
173C LEU* 3.9 22.2 - - + -
158D LEU* 4.6 1.1 - - + -
165D LEU* 3.1 30.2 + - + +
166D GLY* 3.2 4.7 + - - +
168D TYR* 1.3 78.6 - - + +
170D PHE* 1.3 56.4 + - - +
172D ARG* 3.1 1.1 + - - -
173D LEU* 2.6 43.0 + - + +
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Residues in contact with PHE 170 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168B TYR* 3.4 16.3 - + + -
96D THR* 4.6 5.8 - - + -
100D MET* 5.1 1.6 - - + -
151D HIS* 3.3 40.8 - + + -
154D ASN* 3.8 25.6 - - + -
155D LEU* 3.4 36.3 - - + -
158D LEU* 5.3 3.4 - - + -
166D GLY 3.1 14.6 + - - +
167D GLU 3.9 4.9 - - - +
168D TYR 3.3 0.2 - - - -
169D LEU* 1.3 76.5 - - - +
171D GLU* 1.3 58.6 + - - +
174D THR* 2.7 56.3 + - + -
175D LEU* 3.1 36.5 + - + -
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Residues in contact with GLU 171 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154C ASN* 5.4 0.5 - - - +
47D ALA 5.8 0.2 - - - -
48D LEU* 3.8 24.6 - - + +
49D GLU 3.7 7.2 + - - -
50D GLY* 2.8 39.2 + - - +
51D VAL* 3.9 11.2 - - + +
167D GLU 3.4 14.5 + - - +
168D TYR* 3.8 6.4 - - - +
169D LEU 3.3 0.2 - - - -
170D PHE* 1.3 80.0 - - + +
172D ARG* 1.3 104.3 + - - +
175D LEU* 4.1 11.3 - - + +
176D LYS* 3.1 23.0 + - - -
177D HIS* 4.2 1.4 + - - -
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Residues in contact with ARG 172 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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173C LEU* 2.7 51.3 + - + -
174C THR* 3.8 16.8 + - - +
176C LYS* 4.3 3.2 - - - +
49D GLU* 4.5 12.1 + - - +
168D TYR* 3.0 52.4 + - + +
169D LEU 3.5 1.8 - - - +
171D GLU* 1.3 117.1 + - - +
173D LEU* 1.3 79.1 + - + +
174D THR 3.6 0.2 - - - -
176D LYS* 3.6 17.5 - - - +
177D HIS* 3.2 43.3 + - - -
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Residues in contact with LEU 173 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168B TYR* 3.4 11.2 - - + +
169B LEU* 3.7 29.8 - - + -
172B ARG* 3.0 34.2 + - + -
173B LEU* 3.7 28.3 - - + -
173C LEU* 3.7 20.9 - - + -
169D LEU* 2.6 26.6 + - + +
172D ARG* 1.3 92.7 - - + +
174D THR* 1.3 57.2 + - - +
176D LYS* 3.2 14.3 - - - +
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Residues in contact with THR 174 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168B TYR* 2.8 29.2 + - - -
172B ARG* 4.0 14.9 + - - +
147D LYS* 5.9 0.4 - - - +
151D HIS* 3.7 20.2 - - + +
154D ASN* 5.5 1.0 - - - -
170D PHE* 2.7 49.2 + - + -
172D ARG 3.6 0.2 - - - -
173D LEU* 1.3 72.8 - - - +
175D LEU* 1.3 69.7 + - - +
176D LYS* 3.3 14.0 + - - +
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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