Contacts of the strand formed by residues 160 - 167 (chain A) in PDB entry 4LL1
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 VAL 160 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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158A ALA 3.9 7.9 - - - +
159A PRO* 1.3 80.9 - - - +
161A SER* 1.3 67.0 + - - +
183A ARG* 3.3 2.9 - - - +
184A ILE* 2.8 46.7 + - + +
186A ARG 4.1 19.3 - - - +
187A LYS* 4.2 14.6 - - + +
292A LEU* 4.2 30.1 - - + +
293A PRO* 5.6 2.7 - - + +
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Residues in contact with SER 161 (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 4.3 0.2 - - - -
160A VAL* 1.3 81.3 - - - +
162A ALA* 1.3 60.3 + - - +
182A ALA 3.3 11.9 - - - -
183A ARG* 4.2 32.2 + - - -
292A LEU* 5.1 0.7 - - - -
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Residues in contact with ALA 162 (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* 1.3 74.3 - - - +
163A LYS* 1.3 59.1 + - - +
181A SER* 3.3 3.3 + - - -
182A ALA 2.7 38.9 + - - +
290A LEU* 3.7 19.6 - - + +
292A LEU* 3.4 30.2 - - + +
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Residues in contact with LYS 163 (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* 1.3 75.2 - - - +
164A LYS* 1.3 72.9 + - - +
165A GLU* 4.1 23.8 + - - +
179A SER* 5.4 4.2 - - - -
180A VAL 3.2 9.6 - - - +
181A SER* 3.8 17.0 - - - +
290A LEU* 3.7 6.9 - - - +
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Residues in contact with LYS 164 (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* 1.3 81.6 - - - +
165A GLU* 1.3 66.3 + - - +
166A LYS* 5.9 0.7 - - + -
179A SER* 3.3 2.7 - - - -
180A VAL* 2.7 39.3 + - + +
288A VAL* 3.7 21.9 - - + +
289A ILE* 2.9 31.5 + - - +
290A LEU* 3.7 15.9 - - + +
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Residues in contact with GLU 165 (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* 4.1 19.5 + - - +
164A LYS* 1.3 81.2 - - - +
166A LYS* 1.3 64.5 + - - +
177A ARG* 2.8 51.1 + - + +
178A VAL 3.4 10.1 - - - +
179A SER* 3.9 14.9 - - - -
288A VAL* 4.7 0.4 - - - -
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Residues in contact with LYS 166 (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* 5.9 0.4 - - + -
165A GLU* 1.3 75.6 - - - +
167A LYS* 1.3 69.3 + - - +
168A VAL* 3.6 17.9 + - + +
177A ARG* 3.3 8.2 - - - +
178A VAL 2.8 31.7 + - - -
282A VAL* 4.9 1.1 - - - -
285A SER* 3.9 9.3 - - - -
286A LYS* 2.6 47.9 + - + +
287A LYS 4.3 7.4 - - - +
288A VAL* 3.7 31.4 - - + -
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Residues in contact with LYS 167 (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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166A LYS* 1.3 79.9 - - - +
168A VAL* 1.3 65.9 + - - +
169A SER* 3.9 13.2 + - - +
174A PRO 3.4 23.6 + - - +
175A ASP* 4.4 10.3 - - - +
176A GLY 3.5 13.2 - - - +
177A ARG* 4.1 24.0 - - - +
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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