Contacts of the strand formed by residues 187 - 191 (chain B) in PDB entry 4L28
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 GLU 187 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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164B ARG* 2.9 48.0 + - + +
165B CYS 2.7 12.7 + - - +
166B ILE* 3.8 18.0 - - + +
167B ILE* 2.9 26.7 + - - +
185B GLY 3.8 3.6 + - - +
186B ALA* 1.3 75.8 - - - +
188B ILE* 1.3 62.6 + - - +
189B VAL* 6.0 1.3 - - + -
504D GLU* 4.8 4.5 - - - +
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Residues in contact with ILE 188 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167B ILE* 3.6 8.5 - - + +
169B MET* 4.8 11.2 - - - -
178B VAL* 3.5 39.7 - - + +
181B LEU* 3.7 22.4 - - + -
182B ARG* 4.0 10.5 - - + +
186B ALA 3.7 8.7 - - - +
187B GLU* 1.3 81.5 - - - +
189B VAL* 1.3 70.5 + - - +
190B ARG* 3.8 24.5 - - - -
503D LEU* 3.8 7.5 - - - +
504D GLU* 3.6 40.7 + - + +
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Residues in contact with VAL 189 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166B ILE* 4.3 11.7 - - + -
167B ILE 2.8 10.5 + - - +
168B VAL* 3.2 11.1 - - + -
169B MET 2.9 24.3 + - - -
187B GLU* 6.0 0.9 - - + -
188B ILE* 1.3 81.2 - - - +
190B ARG* 1.3 75.7 + - - +
206B VAL* 4.0 24.7 - - + -
210B LEU* 4.1 17.9 - - + -
503D LEU 4.0 3.6 - - - +
507D HIS* 5.3 2.7 - - + -
536D ALA* 4.0 30.7 - - + -
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Residues in contact with ARG 190 (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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169B MET* 3.1 29.7 + - - +
170B PRO 2.9 20.4 + - - -
171B GLU* 3.3 28.9 + - + -
173B MET* 3.1 28.1 + - - +
178B VAL* 3.2 21.2 - - - +
188B ILE* 3.8 7.6 - - - -
189B VAL* 1.3 82.6 - - - +
191B THR* 1.3 67.5 + - - +
503D LEU 3.6 8.6 + - - +
504D GLU 3.1 43.2 + - - +
505D MET* 3.7 19.0 + - - +
506D ASP 4.1 7.2 - - - -
507D HIS* 3.1 28.1 - - - +
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Residues in contact with THR 191 (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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168B VAL* 3.7 11.0 - - + -
169B MET 3.0 4.9 + - - -
170B PRO* 3.2 12.0 - - - +
171B GLU* 2.7 35.7 + - - +
190B ARG* 1.3 80.8 - - - +
192B PRO* 1.3 71.0 + - + +
201B GLU 3.2 22.2 - - - +
203B HIS* 3.4 39.6 + - - +
206B VAL* 3.7 16.8 - - + -
507D HIS* 4.8 0.7 - - + -
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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