Contacts of the strand formed by residues 173 - 177 (chain B) in PDB entry 3B4M
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 SER 173 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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169B ALA 3.0 20.5 + - - -
170B ASP 3.8 9.7 - - - +
171B ALA 3.4 2.5 - - - +
172B ARG* 1.3 76.9 - - - +
174B ILE* 1.3 64.4 + - - +
217B TYR* 5.3 4.3 - - - +
218B ILE 3.1 7.5 + - - -
219B GLU* 3.3 20.4 - - - +
226B VAL* 4.2 6.6 - - - +
246B PRO* 3.8 4.3 - - - +
247B LYS* 3.0 42.7 + - - +
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Residues in contact with ILE 174 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172B ARG 4.5 0.2 + - - -
173B SER* 1.3 77.1 - - - +
175B TYR* 1.3 64.9 + - - +
176B VAL* 4.0 3.6 - - + -
192B PHE* 3.6 30.7 - - + -
217B TYR* 3.3 13.9 - - - +
218B ILE* 2.8 59.7 + - + +
220B PHE* 3.8 15.0 - - + -
226B VAL* 4.0 15.7 - - + +
229B SER* 3.3 25.6 - - - +
230B LEU* 4.5 1.6 - - + -
244B VAL* 3.9 16.6 - - + -
245B ILE 3.7 9.4 - - - +
246B PRO* 4.1 2.9 - - + -
247B LYS* 4.1 2.0 - - - +
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Residues in contact with TYR 175 (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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174B ILE* 1.3 74.6 - - - +
176B VAL* 1.3 64.9 + - - +
177B GLY* 3.3 31.3 - - - -
178B ASN 5.1 0.2 + - - -
215B PHE* 3.6 42.9 - + + +
216B ALA 3.7 2.9 - - - -
217B TYR* 3.9 18.6 - + + -
243B LYS* 3.5 11.0 - - + +
244B VAL* 3.5 2.6 - - - -
245B ILE* 2.8 61.9 + - + +
246B PRO 5.2 1.1 - - - +
247B LYS* 4.3 6.9 - - - +
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Residues in contact with VAL 176 (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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174B ILE* 4.0 7.4 - - + +
175B TYR* 1.3 79.8 - - - +
177B GLY* 1.3 62.3 + - - +
179B VAL* 3.7 21.3 - - + +
188B LEU* 4.4 10.3 - - + -
192B PHE* 4.0 15.9 - - + -
215B PHE* 3.1 8.6 - - - -
216B ALA* 2.9 40.1 + - + +
218B ILE* 3.9 27.6 - - + -
242B ILE* 4.1 23.6 - - + -
243B LYS 3.4 3.4 - - - +
244B VAL* 4.7 2.7 - - + -
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Residues in contact with GLY 177 (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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175B TYR* 3.3 29.4 - - - -
176B VAL* 1.3 73.6 - - - +
178B ASN* 1.3 73.5 + - - +
215B PHE* 4.1 2.2 - - - -
242B ILE* 3.5 6.9 - - - +
243B LYS* 2.7 35.9 + - - -
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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