Contacts of the helix formed by residues 162 - 177 (chain B) in PDB entry 1EFA
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 SER 162 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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160B ILE 3.7 1.0 + - - -
161B PHE* 1.3 70.1 - - - +
163B HIS* 1.3 63.4 + - - +
164B GLU* 3.0 8.3 + - - +
165B ASP* 2.5 39.6 + - - +
166B GLY* 3.0 17.0 + - - -
273B TYR* 4.2 1.6 + - - -
318B LEU* 4.2 27.3 - - - +
319B LEU 2.9 19.8 + - - -
320B PRO* 5.1 1.1 - - - -
321B VAL* 3.8 8.4 - - - +
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Residues in contact with HIS 163 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152B ASP* 3.3 30.0 + - - -
160B ILE* 4.2 7.0 - - + -
161B PHE* 2.8 17.6 + - - +
162B SER* 1.3 70.3 - - - +
164B GLU* 1.3 88.8 + - + +
167B THR* 2.7 37.8 + - - +
196B LEU* 3.5 62.9 + - + +
197B ARG* 4.5 9.2 - - + +
199B ALA* 6.1 1.6 - - + -
200B GLY* 5.0 3.4 - - - -
273B TYR* 3.8 13.5 - - - +
318B LEU* 5.8 2.2 - - + +
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Residues in contact with GLU 164 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152B ASP* 4.6 4.2 - - - +
162B SER* 3.9 8.5 - - - +
163B HIS* 1.3 108.8 - - + +
165B ASP* 1.3 62.6 + - - +
167B THR* 3.2 5.0 + - - -
168B ARG* 3.2 25.2 + - - +
200B GLY* 5.6 3.1 - - - -
203B LYS* 2.5 42.1 + - - +
204B TYR* 3.0 24.3 - - - +
318B LEU* 6.0 3.1 - - + -
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Residues in contact with ASP 165 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
162B SER* 2.5 29.8 + - - +
164B GLU* 1.3 79.6 - - - +
166B GLY* 1.3 58.9 + - - +
168B ARG* 3.5 32.8 + - - +
169B LEU* 2.9 37.1 + - + +
320B PRO* 5.6 3.0 - - - +
321B VAL* 3.7 16.8 - - + +
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Residues in contact with GLY 166 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
162B SER 3.0 10.1 + - - -
163B HIS 3.3 0.4 + - - -
165B ASP* 1.3 77.8 - - - +
167B THR* 1.3 56.2 + - - +
169B LEU* 3.4 1.6 + - - -
170B GLY* 3.0 23.2 + - - -
201B TRP* 5.4 0.2 + - - -
273B TYR* 3.3 24.8 - - - -
289B ILE* 3.5 20.1 - - - +
321B VAL* 3.6 13.2 - - - +
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Residues in contact with THR 167 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163B HIS 2.7 24.1 + - - +
164B GLU 3.2 4.9 + - - -
166B GLY* 1.3 72.6 - - - +
168B ARG* 1.3 63.9 + - - +
170B GLY* 3.3 0.6 + - - +
171B VAL* 2.9 34.5 + - - +
197B ARG* 3.3 40.6 - - + +
200B GLY* 3.3 29.5 + - - -
201B TRP* 3.5 22.8 - - + +
204B TYR* 3.8 2.9 - - - -
273B TYR* 4.1 4.9 + - + -
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Residues in contact with ARG 168 (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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164B GLU 3.2 16.8 + - - +
165B ASP* 3.5 30.5 + - - +
167B THR* 1.3 83.0 + - - +
169B LEU* 1.3 80.5 + - - +
171B VAL 3.2 0.7 + - - -
172B GLU* 2.7 73.5 + - - +
204B TYR* 3.4 40.4 - - + -
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Residues in contact with LEU 169 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165B ASP* 2.9 24.7 + - + +
166B GLY* 3.5 6.1 - - - +
168B ARG* 1.3 104.5 - - - +
170B GLY* 1.3 64.0 + - - +
172B GLU* 4.2 5.7 - - - +
173B HIS* 3.0 25.6 + - - +
289B ILE* 4.0 8.1 - - + -
321B VAL* 4.3 9.9 - - + +
322B SER* 3.8 13.5 - - - -
323B LEU* 3.8 39.6 - - + +
175C VAL* 6.3 2.7 - - + -
176C ALA* 6.0 1.2 - - - -
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Residues in contact with GLY 170 (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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166B GLY 3.0 14.7 + - - -
167B THR* 3.3 3.1 + - - -
168B ARG 3.2 0.2 - - - -
169B LEU* 1.3 77.5 - - - +
171B VAL* 1.3 61.7 + - - +
173B HIS* 3.1 7.8 + - - +
174B LEU* 3.1 25.6 + - - +
201B TRP* 5.7 0.4 - - - -
243B LEU* 3.9 19.0 - - - +
271B VAL* 4.6 9.1 - - - +
289B ILE* 4.1 9.6 - - - +
323B LEU* 5.3 1.1 - - - -
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Residues in contact with VAL 171 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167B THR 2.9 24.4 + - - +
168B ARG 3.8 2.0 - - - +
170B GLY* 1.3 71.4 - - - -
172B GLU* 1.3 65.3 + - + +
173B HIS 3.2 0.2 + - - -
174B LEU* 3.2 5.8 + - - +
175B VAL* 2.9 32.7 + - + +
201B TRP* 4.0 15.5 - - + +
204B TYR* 3.7 32.3 - - + +
205B LEU* 3.8 29.4 - - + -
208B ASN* 4.2 4.0 - - - +
243B LEU* 3.8 26.6 - - + +
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Residues in contact with GLU 172 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168B ARG* 2.7 59.7 + - + +
169B LEU* 4.2 6.6 - - - +
171B VAL* 1.3 77.0 - - + +
173B HIS* 1.3 56.5 + - - +
175B VAL* 3.8 6.9 - - - +
176B ALA* 2.9 30.7 + - - +
204B TYR* 4.9 4.5 - - + -
208B ASN* 5.1 10.9 - - - +
176C ALA* 3.7 18.3 - - + +
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Residues in contact with HIS 173 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169B LEU 3.0 20.0 + - - +
170B GLY* 3.4 6.1 - - - +
171B VAL 3.1 0.2 - - - -
172B GLU* 1.3 74.9 - - - +
174B LEU* 1.3 69.5 + - + +
176B ALA* 3.4 2.9 + - - +
177B LEU* 3.2 39.9 + - + +
271B VAL* 4.8 3.1 - - + -
287B THR* 4.3 11.9 - - + +
323B LEU* 3.6 12.6 - - + +
325B LYS* 3.7 30.0 - - + +
329B THR* 2.8 37.8 + - + -
176C ALA* 2.8 29.8 + - - +
177C LEU* 4.1 7.3 - - + -
331C ALA* 4.6 6.3 - - + -
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Residues in contact with LEU 174 (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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170B GLY 3.1 10.4 + - - +
171B VAL 3.8 6.1 - - - +
173B HIS* 1.3 81.4 - - + +
175B VAL* 1.3 62.9 + - - +
177B LEU* 3.1 7.6 + - + -
179B HIS* 3.0 38.9 + - + -
182B ILE* 4.2 24.7 - - + -
241B ALA* 3.8 31.4 - - + -
242B MET 4.5 3.8 - - - +
243B LEU* 3.7 33.4 - - + -
269B SER* 4.3 2.2 - - - -
271B VAL* 3.9 22.9 - - + -
329B THR* 4.2 14.6 - - + -
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Residues in contact with VAL 175 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171B VAL* 2.9 26.9 + - + +
172B GLU* 3.8 5.8 - - - +
174B LEU* 1.3 72.3 - - - +
176B ALA* 1.3 54.5 + - - +
177B LEU 3.0 1.8 - - - -
178B GLY* 2.6 22.3 + - - -
179B HIS 4.3 7.4 - - - +
182B ILE* 5.2 3.1 - - + -
208B ASN* 3.8 32.8 - - + +
210B ILE* 3.7 29.4 - - + -
325C LYS* 2.6 26.3 + - + +
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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
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172B GLU 2.9 18.6 + - - +
173B HIS 3.9 1.6 - - - +
175B VAL* 1.3 79.3 - - - +
177B LEU* 1.3 59.1 + - - +
178B GLY 3.0 1.3 + - - -
173C HIS* 3.3 36.7 + - - +
176C ALA* 3.9 14.6 - - + -
177C LEU* 3.3 27.4 - - + +
325C LYS* 3.6 7.8 - - - +
329C THR 5.0 2.9 - - - +
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Residues in contact with LEU 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 HIS* 3.2 37.8 + - + +
174B LEU* 3.1 10.5 + - - +
175B VAL 3.0 1.0 - - - -
176B ALA* 1.3 76.9 - - - +
178B GLY* 1.3 60.5 + - - +
179B HIS* 3.5 22.6 + - + +
329B THR* 3.5 30.1 - - - +
331B ALA 5.3 6.3 - - - +
177C LEU* 3.2 26.9 - - + -
329C THR 5.2 2.0 - - - +
330C LEU* 4.7 6.5 - - + -
331C ALA* 4.0 20.6 - - + +
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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