Contacts of the strand formed by residues 256 - 264 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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235B GLY* 5.2 0.7 - - - -
236B VAL* 3.3 12.1 - - - +
237B ASP 4.0 6.1 - - - +
238B ARG 4.0 2.2 - - - -
239B VAL* 3.2 30.7 - - + +
252B ALA 3.0 16.7 + - - +
253B VAL* 3.4 13.0 - - - +
254B LYS 4.4 1.6 - - - +
255B MET* 1.3 79.6 - - - +
257B LYS* 1.3 65.5 + - - +
258B PRO* 3.9 1.0 - - - +
260B GLY* 4.7 2.5 - - - -
261B ILE 3.8 20.6 - - - +
262B ILE* 3.9 12.3 - - + -
288B LYS* 3.2 38.5 + - + -
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Residues in contact with LYS 257 (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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304A ARG* 5.0 1.0 - - - +
169B SER* 4.7 1.8 + - - -
234B LYS* 3.4 28.9 - - - +
235B GLY 3.5 18.5 + - - -
236B VAL 2.9 20.9 + - - +
237B ASP* 2.9 38.3 + - - +
256B VAL* 1.3 74.1 - - - +
258B PRO* 1.3 77.1 - - + +
260B GLY* 2.8 23.5 + - - +
288B LYS* 3.7 8.2 - - - +
97D ARG* 3.9 28.3 - - - +
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Residues in contact with PRO 258 (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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234B LYS 5.8 0.7 - - - +
256B VAL 4.2 3.1 - - - +
257B LYS* 1.3 86.2 - - + +
259B GLY* 1.3 58.8 + - - +
286B ALA 3.2 13.7 - - - +
288B LYS* 3.8 11.8 - - - +
94D GLU* 6.2 0.7 - - + -
97D ARG* 2.9 32.0 + - - +
99D TYR* 4.9 0.9 - - - -
102D HIS* 3.7 30.2 - - + +
105D GLY* 5.0 0.9 - - - -
106D MET* 4.0 35.0 - - + +
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Residues in contact with GLY 259 (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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238B ARG* 4.4 6.9 + - - -
257B LYS 3.3 0.2 + - - -
258B PRO* 1.3 70.4 - - - +
260B GLY* 1.3 64.0 + - - +
261B ILE* 4.6 3.8 - - - +
286B ALA 2.9 12.9 + - - -
287B HIS* 3.0 23.0 + - - +
97D ARG* 4.5 4.8 + - - -
99D TYR* 3.6 39.9 + - - -
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Residues in contact with GLY 260 (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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237B ASP* 3.4 17.5 - - - -
238B ARG* 3.9 4.7 - - - -
256B VAL* 4.7 5.2 - - - -
257B LYS* 2.8 21.1 + - - -
258B PRO 3.1 1.4 + - - -
259B GLY* 1.3 84.5 - - - +
261B ILE* 1.3 64.3 + - - +
287B HIS 3.2 11.8 + - - +
288B LYS* 3.5 3.0 - - - +
289B THR* 3.2 10.7 + - - -
97D ARG* 4.7 1.3 - - - +
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Residues in contact with ILE 261 (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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161B LEU 4.0 16.8 - - - +
162B ALA* 3.5 22.8 - - - +
163B ASP* 3.6 21.1 - - + +
237B ASP 3.5 5.5 + - - -
238B ARG* 3.4 28.3 - - - +
239B VAL 3.0 23.0 + - - +
256B VAL* 3.8 2.4 - - - +
259B GLY 4.6 3.1 - - - +
260B GLY* 1.3 79.9 - - - +
262B ILE* 1.3 75.8 + - - +
289B THR* 3.5 20.2 - - + +
291B LYS* 4.2 17.5 - - + +
99D TYR* 6.2 0.2 - - - +
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Residues in contact with ILE 262 (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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239B VAL* 3.2 7.9 - - + +
241B MET* 3.5 31.6 - - + -
249B LEU* 4.5 5.6 - - + -
252B ALA* 3.8 10.8 - - + -
253B VAL* 3.6 47.8 - - + +
256B VAL* 3.9 20.0 - - + -
261B ILE* 1.3 78.5 - - - +
263B SER* 1.3 61.7 + - - +
264B ASN 5.0 0.4 - - - +
288B LYS* 5.1 4.9 - - + -
289B THR 2.7 14.3 + - - +
290B ILE* 3.5 17.2 - - + -
291B LYS* 2.8 29.3 + - - +
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Residues in contact with SER 263 (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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158B GLY* 2.9 34.9 + - - -
161B LEU* 3.4 19.4 - - - +
162B ALA* 3.8 20.0 - - - -
239B VAL 2.7 13.0 + - - -
240B ILE* 3.3 6.3 - - - +
241B MET 2.8 25.3 + - - -
261B ILE 4.1 0.4 - - - -
262B ILE* 1.3 73.2 - - - +
264B ASN* 1.3 61.3 + - - +
265B ILE 3.7 1.2 + - - -
291B LYS* 3.7 5.6 - - - -
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Residues in contact with ASN 264 (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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161B LEU* 4.6 1.6 - - - +
241B MET* 3.4 26.6 - - + +
262B ILE* 3.9 1.0 + - + +
263B SER* 1.3 73.7 + - - +
265B ILE* 1.3 61.5 + - - +
266B ASN* 2.9 35.5 + - - +
268B HIS* 2.9 28.5 + - - -
274B LEU* 5.9 0.9 - - - -
290B ILE* 5.8 2.9 - - + -
291B LYS 2.7 20.5 + - - +
292B GLY* 3.1 26.5 - - - -
293B GLY 3.3 7.3 + - - +
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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