Contacts of the strand formed by residues 237 - 243 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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169A LYS 2.9 11.0 + - - +
170A HIS* 5.1 8.1 - - + +
171A TRP* 3.0 31.4 + - - -
226A TYR* 3.9 1.7 + - - -
235A GLN 5.6 0.4 - - - +
236A GLY* 1.3 79.1 - - - +
238A VAL* 1.3 64.6 + - - +
308A ASP* 3.3 22.7 + - + +
309A TYR* 3.6 35.1 - - + -
381A THR* 6.1 2.8 - - - +
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Residues in contact with VAL 238 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128A LEU* 5.7 0.2 - - + -
161A PHE* 4.2 11.9 - - + -
171A TRP* 3.5 24.9 - - + -
172A PHE 4.7 0.2 - - - -
173A THR* 3.8 17.0 - - + +
223A VAL* 3.8 27.0 - - + +
226A TYR* 3.8 34.8 - - + -
237A LYS* 1.3 80.7 - - - +
239A GLY* 1.3 70.4 + - - +
306A SER 4.1 3.3 - - - +
307A ALA* 3.8 3.6 - - - -
308A ASP* 2.8 36.8 + - - +
309A TYR* 4.2 0.9 - - - -
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Residues in contact with GLY 239 (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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171A TRP 2.9 11.5 + - - -
172A PHE* 3.8 6.1 - - - -
173A THR* 3.0 26.2 + - - -
219A HIS* 3.5 9.1 - - - -
238A VAL* 1.3 74.7 - - - +
240A ILE* 1.3 61.0 + - - -
307A ALA* 4.4 2.9 - - - -
308A ASP 4.3 1.8 - - - -
309A TYR* 3.4 29.4 - - - -
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Residues in contact with ILE 240 (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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172A PHE* 3.7 3.9 - - - -
173A THR* 3.7 17.9 - - - +
174A PHE* 4.0 27.1 - - + +
177A PRO* 4.6 7.2 - - + -
215A PHE* 5.3 2.7 - - + +
216A LEU* 5.3 7.2 - - + -
219A HIS* 3.8 18.8 - - + +
239A GLY* 1.3 76.1 - - - +
241A VAL* 1.3 63.4 + - - +
242A LEU* 4.2 25.9 - - + +
271A TYR* 5.7 0.2 - - + -
275A LEU* 3.6 29.8 - - + -
307A ALA* 4.2 12.3 - - + -
309A TYR 3.7 1.6 + - - -
310A ILE* 4.6 3.8 - - + -
311A GLY* 2.8 30.3 + - - +
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Residues in contact with VAL 241 (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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86A ARG* 3.6 20.9 - - - +
127A ASN* 3.8 2.2 - - - +
172A PHE* 3.5 33.2 - - + -
174A PHE 3.0 16.2 + - - +
175A ASN* 3.3 18.6 - - - +
176A GLN 2.9 23.8 + - - +
177A PRO* 3.4 9.2 - - - +
240A ILE* 1.3 72.4 - - - +
242A LEU* 1.3 62.8 + - - +
311A GLY 3.5 2.0 - - - +
313A ASN* 3.2 32.8 - - - +
385A THR* 3.4 13.5 - - + +
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Residues in contact with LEU 242 (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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176A GLN* 4.6 2.0 - - - +
177A PRO* 3.8 21.1 - - + -
240A ILE* 4.2 20.0 - - + -
241A VAL* 1.3 82.5 - - - +
243A ASP* 1.3 63.7 + - - +
244A PHE 3.7 0.2 + - - -
268A ILE* 3.7 28.9 - - + -
271A TYR* 3.8 33.7 - - + -
272A LEU* 3.9 21.5 - - + -
275A LEU* 4.2 8.3 - - + -
310A ILE* 4.2 9.6 - - + -
311A GLY 2.8 10.9 + - - +
312A ILE* 3.3 7.9 - - + +
313A ASN* 2.9 23.1 + - - -
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Residues in contact with ASP 243 (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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176A GLN* 3.5 42.6 - - - +
178A ARG* 2.9 45.1 + - - +
179A ILE* 3.7 14.3 - - - +
242A LEU* 1.3 75.4 - - - +
244A PHE* 1.3 62.0 + - - +
245A ASN* 5.2 6.1 + - - +
267A HIS* 2.9 24.4 + - - +
268A ILE* 3.8 8.0 - - - +
313A ASN* 3.5 11.2 - - - +
315A TYR* 6.1 0.4 - - + -
1005A GOL 4.5 5.2 - - - +
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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