Contacts of the strand formed by residues 177 - 184 (chain A) in PDB entry 4LL4
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 ARG 177 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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165A GLU* 3.3 42.7 + - + +
166A LYS 3.4 5.8 - - - +
167A LYS* 4.8 12.9 - - - +
168A VAL 4.8 0.4 - - - -
175A ASP* 3.3 38.5 + - - +
176A GLY* 1.3 75.6 + - - +
178A VAL* 1.3 68.1 + - - +
179A SER* 4.4 0.4 - - - -
202A GLU* 4.7 4.0 - - + +
203A ASN* 3.8 0.5 - - - -
204A THR* 2.9 36.4 + - + +
205A SER* 3.5 3.1 + - - +
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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
----------------------------------------------------------
164A LYS 3.9 0.3 - - - +
165A GLU* 3.4 2.5 - - - -
166A LYS* 2.8 37.7 + - - +
168A VAL* 4.3 11.7 - - + -
177A ARG* 1.3 81.7 - - - +
179A SER* 1.3 66.3 + - - +
202A GLU 3.4 9.9 - - - +
203A ASN* 3.8 17.5 - - - +
205A SER* 4.2 10.1 - - - +
209A VAL* 4.3 14.1 - - + -
280A VAL* 4.0 29.8 - - + -
282A VAL* 4.5 4.0 - - + -
288A VAL* 4.1 20.5 - - + +
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Residues in contact with SER 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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164A LYS 3.2 13.7 - - - -
165A GLU* 3.5 20.3 + - - +
177A ARG* 6.1 0.2 - - - -
178A VAL* 1.3 82.1 - - - +
180A VAL* 1.3 66.3 + - - +
200A ASP 4.3 0.6 + - - -
201A PHE* 3.1 9.8 - - - +
202A GLU* 2.9 55.4 + - - +
280A VAL* 4.5 0.5 - - - +
288A VAL* 5.1 0.2 - - - -
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Residues in contact with VAL 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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163A LYS* 3.4 1.7 - - - +
164A LYS* 2.7 39.7 + - + +
179A SER* 1.3 79.7 - - - +
181A SER* 1.3 65.3 + - - +
200A ASP 3.3 5.2 - - - -
201A PHE* 3.5 30.1 - - + -
278A ILE* 3.8 22.7 - - + +
280A VAL* 4.0 6.7 - - + -
288A VAL* 3.8 28.7 - - + +
290A LEU* 3.8 22.5 - - + +
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Residues in contact with SER 181 (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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162A ALA 3.3 10.6 + - - -
163A LYS* 3.9 13.5 - - - +
179A SER* 6.3 0.4 - - - -
180A VAL* 1.3 74.3 - - - +
182A ALA* 1.3 61.0 + - - +
183A ARG* 5.7 4.4 + - - +
198A HIS 4.0 0.2 - - - +
199A ALA* 3.1 5.2 - - - +
200A ASP* 2.9 47.6 + - - -
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Residues in contact with ALA 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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161A SER* 3.1 3.8 - - - -
162A ALA 2.8 31.9 + - - +
181A SER* 1.3 74.6 + - - +
183A ARG* 1.3 66.3 - - - +
198A HIS 3.3 6.3 - - - +
199A ALA* 4.1 5.6 - - + -
278A ILE* 3.4 26.9 - - + -
290A LEU* 3.3 26.7 - - + -
292A LEU* 4.6 5.8 - - + +
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Residues in contact with ARG 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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159A PRO* 6.2 2.7 - - + +
160A VAL 3.4 11.2 - - - +
161A SER* 4.1 17.8 + - - +
181A SER* 5.7 4.4 + - - +
182A ALA* 1.3 79.3 - - - +
184A ILE* 1.3 70.0 + - - +
196A SER 3.8 0.7 - - - +
197A ILE* 3.7 1.8 - - - +
198A HIS* 2.5 73.3 + - + +
292A LEU* 5.9 0.9 - - - -
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Residues in contact with ILE 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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159A PRO* 3.5 6.1 - - - +
160A VAL* 2.9 52.0 + - + +
183A ARG* 1.3 79.6 - - - +
185A ASP* 1.3 63.8 + - - +
186A ARG 3.4 20.0 - - - +
189A PHE* 4.3 4.5 - - + -
195A ILE* 4.0 16.6 - - + -
196A SER 3.5 18.2 - - - +
197A ILE* 4.3 9.0 - - + -
276A LEU* 4.0 18.4 - - + -
278A ILE* 5.4 0.9 - - + -
292A LEU* 4.7 15.3 - - + -
293A PRO 5.7 0.4 - - - +
294A LEU* 4.1 22.7 - - + -
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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