Contacts of the strand formed by residues 237 - 243 (chain B) in PDB entry 3F4V
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 237 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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169B LYS 2.9 10.1 + - - +
170B HIS* 5.1 7.9 - - + +
171B TRP* 2.9 31.4 + - - -
226B TYR* 3.9 1.4 + - - -
235B GLN 5.6 0.4 - - - +
236B GLY* 1.3 80.6 - - - +
238B VAL* 1.3 65.2 + - - +
308B ASP* 3.3 23.4 + - + +
309B TYR* 3.6 33.9 - - + -
381B THR* 6.1 2.8 - - - +
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Residues in contact with VAL 238 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128B LEU* 5.8 0.2 - - + -
161B PHE* 4.2 8.7 - - + -
171B TRP* 3.5 26.5 - - + -
173B THR* 3.8 29.6 - - + -
223B VAL* 3.8 19.5 - - + +
226B TYR* 3.8 37.2 - - + -
237B LYS* 1.3 80.1 - - - +
239B GLY* 1.3 63.7 + - - +
306B SER 4.1 3.1 - - - +
307B ALA* 3.8 3.5 - - - -
308B ASP* 2.8 36.1 + - - +
309B TYR* 4.2 2.0 - - - -
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Residues in contact with GLY 239 (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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171B TRP 2.9 10.7 + - - -
172B PHE* 3.8 6.5 - - - -
173B THR* 3.0 26.3 + - - -
219B HIS* 3.4 9.0 - - - -
238B VAL* 1.3 74.9 - - - +
240B ILE* 1.3 60.0 + - - -
307B ALA* 4.4 3.4 - - - -
308B ASP 4.3 1.6 - - - -
309B TYR* 3.4 29.1 - - - -
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Residues in contact with ILE 240 (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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172B PHE* 3.7 4.0 - - - -
173B THR* 3.7 11.7 - - - +
174B PHE* 3.9 26.9 - - + +
177B PRO* 4.6 7.2 - - + -
215B PHE* 5.3 2.7 - - + +
216B LEU* 5.3 7.0 - - + -
219B HIS* 3.8 24.7 - - + +
239B GLY* 1.3 75.6 - - - +
241B VAL* 1.3 68.1 + - - +
242B LEU* 4.1 24.4 + - + +
271B TYR* 5.7 0.7 - - + -
275B LEU* 3.6 30.5 - - + -
307B ALA* 4.2 12.3 - - + -
309B TYR 3.8 1.6 + - - -
310B ILE* 3.9 5.7 - - + -
311B GLY* 2.8 25.5 + - - +
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Residues in contact with VAL 241 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86B ARG* 3.7 20.6 - - - +
127B ASN* 3.8 2.0 - - - +
172B PHE* 3.5 33.9 - - + -
174B PHE 3.0 17.0 + - - +
175B ASN* 3.3 11.9 - - - +
176B GLN 2.9 22.9 + - - +
177B PRO* 3.4 9.2 - - - +
240B ILE* 1.3 72.6 - - - +
242B LEU* 1.3 63.4 + - - +
311B GLY 3.5 2.5 - - - -
313B ASN* 3.2 41.5 - - - +
385B THR* 3.5 15.0 - - + +
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Residues in contact with LEU 242 (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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176B GLN* 4.6 2.0 - - - +
177B PRO* 3.8 20.4 - - + -
240B ILE* 4.2 19.5 - - + +
241B VAL* 1.3 81.5 - - - +
243B ASP* 1.3 63.5 + - - +
268B ILE* 3.7 26.9 - - + -
271B TYR* 3.7 37.7 - - + -
272B LEU* 3.9 22.7 - - + -
275B LEU* 4.2 8.3 - - + -
310B ILE* 4.2 8.1 - - + -
311B GLY 2.8 13.0 + - - +
312B ILE* 3.3 9.2 - - + +
313B ASN* 2.9 22.8 + - - -
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Residues in contact with ASP 243 (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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176B GLN* 3.5 43.2 - - - +
177B PRO* 5.3 0.2 - - - +
178B ARG* 2.8 47.2 + - - +
179B ILE* 3.7 12.8 - - - +
242B LEU* 1.3 75.1 - - - +
244B PHE* 1.3 61.3 + - - +
245B ASN* 5.2 5.4 + - - +
267B HIS* 3.0 23.7 + - + +
268B ILE* 3.8 8.0 - - - +
313B ASN* 3.5 11.2 - - - +
315B TYR* 6.1 0.2 - - + -
1005B GOL 4.4 6.1 - - - +
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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
------------------------------------------------------------
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