Contacts of the strand formed by residues 256 - 264 (chain A) in PDB entry 3FTN
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 256 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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235A GLY* 5.1 0.7 - - - -
236A VAL 3.4 8.7 - - - +
237A ASP 4.9 0.4 - - - +
238A ARG 4.4 3.1 - - - -
239A VAL* 2.9 42.4 - - + +
252A ALA 3.0 17.0 + - - +
253A VAL 3.6 8.7 - - - +
254A LYS 4.3 1.7 - - - +
255A MET* 1.3 78.4 - - - +
257A LYS* 1.3 64.4 + - - +
258A PRO* 4.4 0.5 - - - +
260A GLY* 4.9 7.6 - - - -
261A ILE 4.3 3.1 - - - +
262A ILE* 3.8 22.7 - - + -
288A LYS* 3.1 39.9 + - + -
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Residues in contact with LYS 257 (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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169A SER* 4.6 1.6 + - - -
234A LYS* 3.3 26.0 - - - +
235A GLY 3.4 20.0 - - - -
236A VAL* 2.9 22.4 + - - +
237A ASP* 2.9 36.0 + - - +
255A MET 3.9 0.4 + - - -
256A VAL* 1.3 76.3 - - - +
258A PRO* 1.3 77.8 - - + +
260A GLY* 2.9 22.7 + - - +
288A LYS* 3.7 7.9 - - - +
304B ARG* 5.2 1.0 - - - +
97C ARG* 3.9 24.9 - - - +
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Residues in contact with PRO 258 (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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234A LYS 5.8 0.4 - - - +
256A VAL 4.4 1.8 - - - +
257A LYS* 1.3 90.3 - - + +
259A GLY* 1.3 57.8 + - - +
286A ALA* 3.3 15.5 - - + +
288A LYS* 3.8 8.5 - - - +
94C GLU* 6.2 0.9 - - + -
97C ARG* 2.8 32.5 + - - +
99C TYR* 5.0 0.9 - - - +
102C HIS* 3.7 27.5 - - + +
105C GLY* 4.9 1.8 - - - -
106C MET* 3.8 37.7 - - + +
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Residues in contact with GLY 259 (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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238A ARG* 4.2 8.1 + - - -
258A PRO* 1.3 71.5 - - - +
260A GLY* 1.3 65.0 + - - +
261A ILE* 4.6 3.1 - - - +
286A ALA 3.0 13.7 + - - -
287A HIS* 3.0 13.2 + - - +
97C ARG* 4.2 5.5 + - - -
99C TYR* 3.6 47.6 + - - -
102C HIS* 4.5 0.4 - - - -
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Residues in contact with GLY 260 (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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237A ASP 3.4 16.6 - - - -
238A ARG* 4.0 3.4 - - - -
256A VAL* 4.9 5.6 - - - -
257A LYS* 2.9 20.9 + - - -
258A PRO 3.1 1.0 + - - -
259A GLY* 1.3 83.5 - - - +
261A ILE* 1.3 64.5 + - - +
287A HIS 3.2 2.4 + - - +
288A LYS* 3.6 3.2 - - - +
289A THR* 3.1 22.5 + - - -
97C ARG* 5.2 0.7 - - - -
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Residues in contact with ILE 261 (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 LEU 4.1 15.7 - - - +
162A ALA* 3.7 18.3 - - - +
163A ASP* 3.8 20.4 - - + +
237A ASP 3.5 6.9 + - - -
238A ARG* 3.4 29.7 - - - +
239A VAL 3.1 23.2 + - - +
256A VAL* 4.3 2.3 - - - +
259A GLY 4.6 2.9 - - - +
260A GLY* 1.3 80.6 - - - +
262A ILE* 1.3 74.6 + - - +
263A SER 4.1 0.2 - - - -
289A THR* 3.5 18.8 - - + +
291A LYS* 4.3 20.6 - - + +
99C TYR* 6.0 0.9 - - - +
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Residues in contact with ILE 262 (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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239A VAL* 3.4 7.4 - - + +
241A MET* 3.6 31.4 - - + -
249A LEU* 4.3 6.7 - - + -
252A ALA* 3.9 9.9 - - + -
253A VAL* 3.5 44.9 - - + +
256A VAL* 3.8 26.0 - - + -
261A ILE* 1.3 75.8 - - - +
263A SER* 1.3 62.4 + - - +
264A ASN 4.9 0.2 - - - +
288A LYS* 4.8 6.1 - - + -
289A THR 2.8 13.0 + - - +
290A ILE* 4.1 19.3 - - + -
291A LYS* 2.8 29.3 + - - +
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Residues in contact with SER 263 (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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158A GLY* 2.7 38.7 + - - -
161A LEU* 3.7 13.0 - - - +
162A ALA* 3.7 24.5 - - - -
239A VAL 2.8 11.8 + - - -
240A ILE* 3.3 5.4 - - - +
241A MET 2.8 25.3 + - - -
262A ILE* 1.3 75.8 - - - +
264A ASN* 1.3 59.6 + - - +
291A LYS* 3.8 6.1 - - - -
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Residues in contact with ASN 264 (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 LEU* 4.5 1.6 - - - +
241A MET* 3.6 27.3 - - + +
262A ILE* 4.0 1.0 + - + +
263A SER* 1.3 73.4 - - - +
265A ILE* 1.3 64.9 + - - +
266A ASN* 2.9 35.7 + - - +
268A HIS* 3.0 23.4 + - - -
290A ILE* 5.8 0.4 - - + -
291A LYS 2.7 20.1 + - - +
292A GLY* 3.1 20.4 - - - -
293A GLY 3.3 6.9 + - - -
281C TRP* 4.4 10.5 - - + -
284C GLY* 3.0 25.5 + - - -
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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