Contacts of the strand formed by residues 177 - 184 (chain A) in PDB entry 4EEM
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 LYS 177 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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174A SER 4.4 8.1 - - - +
175A PRO* 3.5 9.6 + - - +
176A HIS* 1.3 72.8 - - - +
178A VAL* 1.3 59.9 + - - +
208A ASP* 3.3 17.7 - - - +
239A TYR* 3.8 25.6 - - + +
240A ASP* 2.7 47.9 + - - +
241A TYR* 3.7 8.0 - - - -
242A THR* 3.0 49.2 + - - +
243A CYS* 3.0 13.1 + - - +
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Residues in contact with VAL 178 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176A HIS* 3.6 29.6 - - + +
177A LYS* 1.3 77.0 - - - +
179A ALA* 1.3 62.8 + - - +
180A ILE* 3.8 12.7 + - + -
207A LEU* 4.6 6.5 - - + -
208A ASP 2.9 6.7 + - - -
209A TYR* 3.1 13.4 - - + +
210A GLY 3.0 24.1 + - - +
241A TYR* 3.3 6.5 - - - -
243A CYS* 3.4 16.2 - - - +
245A VAL* 3.5 30.7 - - + -
260A TYR 3.7 6.7 - - - +
261A ARG* 4.0 13.9 - - + -
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Residues in contact with ALA 179 (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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178A VAL* 1.3 72.9 - - - +
180A ILE* 1.3 61.3 + - - +
181A ILE* 3.9 4.3 - - + +
210A GLY 3.7 4.0 - - - -
212A TYR* 4.1 4.9 - - + -
235A ALA* 3.8 18.6 - - + -
241A TYR* 3.3 34.3 - - + -
243A CYS 2.9 7.1 + - - -
244A PHE* 3.4 17.6 - - + -
245A VAL 3.0 22.5 + - - +
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Residues in contact with ILE 180 (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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178A VAL* 3.8 18.6 - - + +
179A ALA* 1.3 71.7 - - - +
181A ILE* 1.3 59.8 + - - +
182A ILE* 4.6 3.5 - - + +
194A TRP* 3.7 31.6 - - + -
202A LEU* 4.3 17.9 - - + -
207A LEU* 5.5 0.4 - - + -
209A TYR* 3.8 26.0 - - + -
210A GLY 2.8 16.7 + - - +
211A ILE* 3.6 15.7 - - + +
212A TYR* 2.7 34.8 + - - +
245A VAL* 3.5 32.3 - - + +
247A SER* 4.5 7.0 - - - -
260A TYR* 5.1 2.7 - - + +
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Residues in contact with ILE 181 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179A ALA* 3.9 22.0 - - + +
180A ILE* 1.3 79.0 - - - +
182A ILE* 1.3 62.8 + - - +
183A PRO* 4.0 2.8 - - - +
212A TYR* 3.5 17.9 - - + -
214A ILE* 4.0 10.8 - - + -
228A LEU* 4.0 25.0 - - + +
231A GLY* 3.6 40.8 - - - +
235A ALA* 4.3 1.6 - - + -
244A PHE* 4.5 6.5 - - + -
245A VAL 2.8 17.3 + - - +
246A PHE* 3.6 19.7 - - + -
247A SER 3.0 24.8 + - - +
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Residues in contact with ILE 182 (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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180A ILE* 4.6 6.1 - - + +
181A ILE* 1.3 77.0 - - - +
183A PRO* 1.3 74.0 - - + +
184A PHE* 3.9 5.0 - - + +
191A LEU* 4.1 16.8 - - + -
194A TRP* 3.8 49.1 - - + -
211A ILE* 4.4 4.3 - - + -
212A TYR 2.8 16.9 + - - +
213A VAL* 3.7 12.0 - - + -
214A ILE* 2.8 30.4 + - - -
228A LEU* 4.7 1.1 - - - -
247A SER* 3.4 15.7 - - - +
249A VAL* 3.7 25.6 - - + -
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Residues in contact with PRO 183 (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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182A ILE* 1.3 88.8 - - + +
184A PHE* 1.3 57.9 + - - +
214A ILE* 4.0 4.5 - - + +
222A PHE* 4.2 3.8 - - + -
224A ARG* 3.9 27.4 - - + +
227A LEU* 4.1 15.0 - - + -
228A LEU* 3.7 27.7 - - + -
247A SER 3.2 18.4 - - - +
248A ASP* 3.9 13.2 - - - +
249A VAL* 4.6 0.3 - - - +
403A UDP 2.6 43.3 + - - +
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Residues in contact with PHE 184 (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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182A ILE* 3.9 2.2 - - + +
183A PRO* 1.3 75.3 - - - +
185A ARG* 1.3 62.4 + - - +
186A ASN* 3.6 13.9 - - - -
187A ARG* 3.4 42.6 - - + -
188A GLN* 3.5 23.8 - - + -
191A LEU* 3.9 18.2 - - + -
213A VAL* 3.3 31.4 - - + -
214A ILE 3.0 10.5 + - - +
215A ASN* 3.4 21.7 - - - -
216A GLN* 3.0 25.3 + - - +
222A PHE* 3.9 9.8 - - - -
227A LEU* 4.2 0.8 - - - +
249A VAL* 4.4 13.7 - - + -
389A GLN* 4.3 10.1 - - - -
403A UDP 3.2 5.4 - - - -
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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