Contacts of the strand formed by residues 166 - 173 (chain D) in PDB entry 1EFP
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 166 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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181C GLU 3.5 8.7 - - - -
182C VAL 5.1 1.3 - - - -
183C ALA* 5.3 1.8 - - - -
238C ASP* 3.8 11.0 - - - +
162D GLU* 4.0 3.0 - - - +
163D VAL* 2.6 35.2 + - - +
164D ASP 3.3 2.0 + - - -
165D GLY* 1.3 80.7 - - - +
167D LEU* 1.3 70.4 + - - +
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Residues in contact with LEU 167 (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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180C ASP* 3.6 4.5 - - - +
181C GLU* 2.9 59.4 + - + +
148D SER* 5.0 4.3 - - - +
160D THR* 4.9 15.3 - - - +
161D ARG 3.3 9.2 - - - +
162D GLU* 3.3 40.2 - - - +
163D VAL* 3.9 3.1 - - - +
166D GLY* 1.3 78.8 - - - +
168D GLN* 1.3 62.0 + - - +
169D THR* 5.8 0.9 - - - +
183D ARG* 3.9 10.8 - - - +
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Residues in contact with GLN 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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67C HIS* 4.1 28.5 + - - +
69C LEU* 4.6 7.5 - - - +
94C ASP* 5.3 2.8 - - - +
177C TRP* 4.0 10.8 - - + -
179C ALA 3.7 0.7 - - - -
180C ASP* 3.5 16.9 - - - +
160D THR* 3.5 0.6 - - - -
161D ARG* 2.6 72.3 + - + +
163D VAL* 3.7 23.9 - - + +
167D LEU* 1.3 75.1 - - - +
169D THR* 1.3 61.3 + - - +
170D ILE* 3.5 24.8 - - + +
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Residues in contact with THR 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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177C TRP* 3.9 2.1 - - - -
178C VAL* 2.9 36.4 + - + +
179C ALA* 2.8 28.1 + - - +
158D LYS* 4.2 21.8 - - - -
159D VAL 3.7 7.2 - - - +
160D THR* 2.9 34.4 - - + +
167D LEU* 4.3 1.6 - - - +
168D GLN* 1.3 72.9 - - - +
170D ILE* 1.3 74.5 + - - +
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Residues in contact with ILE 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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69C LEU* 3.8 23.3 - - + -
71C GLU* 5.7 0.4 - - - +
175C SER* 5.0 2.2 - - - -
176C SER 3.2 13.7 - - - +
177C TRP* 4.2 5.8 - - + -
178C VAL* 4.3 5.6 - - - +
143D GLN 4.0 19.3 - - - +
144D ALA* 4.7 2.2 - - - -
157D ALA 3.7 0.2 - - - +
158D LYS* 3.5 4.0 - - - -
159D VAL* 3.0 42.4 + - + +
161D ARG* 3.7 24.0 - - - +
168D GLN* 3.5 29.2 - - + +
169D THR* 1.3 81.5 - - - +
171D ALA* 1.3 61.3 + - - +
172D VAL* 4.1 12.1 - - + -
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Residues in contact with ALA 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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174C LEU 4.0 0.7 - - - +
175C SER* 3.3 4.2 - - - -
176C SER* 2.8 46.9 + - - +
178C VAL* 4.3 13.4 - - + +
156D LYS* 4.8 19.3 - - + +
157D ALA 3.2 8.3 - - - +
158D LYS* 4.6 9.6 - - + -
170D ILE* 1.3 75.0 - - - +
172D VAL* 1.3 61.8 + - - +
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Residues in contact with VAL 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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174C LEU 3.7 4.7 - - - -
175C SER* 4.0 11.7 - - - -
142D ALA* 3.6 16.6 - - + -
143D GLN 3.8 23.1 - - - +
144D ALA* 4.7 6.3 - - + -
156D LYS* 3.0 6.5 - - - +
157D ALA* 2.9 47.0 + - + +
159D VAL* 4.7 8.1 - - + -
170D ILE* 4.1 13.7 - - + -
171D ALA* 1.3 78.8 - - - +
173D SER* 1.3 73.4 + - - +
174D LEU* 6.1 0.2 - - + -
176D ALA* 3.9 15.0 - - + -
178D VAL* 5.9 1.8 - - + -
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Residues in contact with SER 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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173C GLY 5.2 2.5 - - - -
174C LEU* 3.2 27.5 + - - +
142D ALA* 3.7 14.7 + - - +
155D ALA 3.7 7.0 - - - -
156D LYS* 4.2 2.9 - - - -
172D VAL* 1.3 78.0 - - - +
174D LEU* 1.3 66.7 + - - +
175D PRO* 3.4 16.4 + - - +
176D ALA* 3.5 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