Contacts of the strand formed by residues 256 - 264 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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228C MET* 5.7 0.6 - - - +
235C GLY* 5.1 0.4 - - - -
236C VAL* 3.3 12.3 - - - +
237C ASP 4.0 8.1 - - - +
238C ARG 4.1 0.4 - - - -
239C VAL* 3.3 30.1 - - + +
252C ALA 3.1 16.9 + - - +
253C VAL 3.6 9.0 - - - +
254C LYS 4.5 1.6 - - - +
255C MET* 1.3 80.2 - - - +
257C LYS* 1.3 63.6 + - - +
258C PRO* 4.2 0.9 - - - +
260C GLY* 4.8 1.6 - - - -
261C ILE 3.9 20.6 - - - +
262C ILE* 3.9 16.6 - - + -
288C LYS* 3.1 44.4 + - + -
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Residues in contact with LYS 257 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97A ARG* 3.8 28.0 - - - +
169C SER* 4.8 1.8 + - - -
234C LYS* 3.2 29.3 - - - +
235C GLY 3.4 20.9 - - - -
236C VAL* 2.9 19.6 + - - +
237C ASP* 3.1 34.5 + - - +
255C MET 3.8 0.2 + - - -
256C VAL* 1.3 76.7 - - - +
258C PRO* 1.3 81.7 - - + +
259C GLY 3.3 0.3 + - - -
260C GLY* 2.9 18.0 + - - +
288C LYS* 3.7 7.2 - - - +
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Residues in contact with PRO 258 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94A GLU* 6.0 1.8 - - + +
97A ARG* 2.9 32.2 + - - +
99A TYR* 4.8 2.3 - - - +
102A HIS* 3.6 32.5 - - + +
105A GLY* 4.7 1.8 - - - -
106A MET* 3.9 36.8 - - + +
234C LYS 5.7 1.1 - - - +
256C VAL 4.2 2.7 - - - +
257C LYS* 1.3 86.0 - - + +
259C GLY* 1.3 56.7 + - - +
286C ALA 3.3 10.8 - - - +
288C LYS* 3.7 10.9 - - - +
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Residues in contact with GLY 259 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97A ARG* 4.3 4.5 + - - -
99A TYR* 3.4 40.7 + - - -
238C ARG* 4.5 5.7 + - - -
257C LYS 3.3 0.2 + - - -
258C PRO* 1.3 71.4 - - - +
260C GLY* 1.3 64.3 + - - +
261C ILE* 4.7 2.9 - - - +
286C ALA 3.0 12.5 + - - -
287C HIS* 3.1 23.6 + - - +
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Residues in contact with GLY 260 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97A ARG* 4.5 3.3 - - - +
237C ASP 3.3 16.8 - - - -
238C ARG* 3.9 4.9 - - - -
256C VAL* 4.7 6.1 - - - -
257C LYS* 2.9 19.2 + - - -
258C PRO 3.2 1.2 + - - -
259C GLY* 1.3 82.9 - - - +
261C ILE* 1.3 64.9 + - - +
287C HIS 3.3 1.8 + - - +
288C LYS* 3.7 3.0 - - - -
289C THR* 3.2 22.1 + - - -
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Residues in contact with ILE 261 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99A TYR* 6.1 0.4 - - - +
161C LEU 3.9 17.3 - - - +
162C ALA* 3.5 21.3 - - - +
163C ASP* 3.6 22.4 - - + +
237C ASP 3.4 6.3 + - - -
238C ARG* 3.3 29.4 - - - +
239C VAL 3.1 22.5 + - - +
256C VAL* 3.9 2.3 - - - +
259C GLY 4.7 2.9 - - - +
260C GLY* 1.3 79.9 - - - +
262C ILE* 1.3 73.8 + - - +
289C THR* 3.6 17.9 - - + +
291C LYS* 4.3 19.1 - - + +
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Residues in contact with ILE 262 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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239C VAL* 3.3 7.4 - - + +
241C MET* 3.6 31.0 - - + -
249C LEU* 4.3 6.7 - - + -
252C ALA* 3.7 13.5 - - + -
253C VAL* 3.6 47.1 - - + +
256C VAL* 3.9 20.9 - - + -
261C ILE* 1.3 76.4 - - - +
263C SER* 1.3 60.8 + - - +
264C ASN 4.9 0.4 - - - +
288C LYS* 4.9 5.2 - - + -
289C THR 2.8 15.2 + - - +
290C ILE* 4.2 17.0 - - + -
291C LYS* 2.8 30.5 + - - +
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Residues in contact with SER 263 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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158C GLY* 2.7 35.1 + - - -
161C LEU* 3.3 20.0 - - - +
162C ALA* 3.9 20.0 - - - -
239C VAL 2.7 13.4 + - - -
240C ILE* 3.2 9.1 - - - +
241C MET* 2.7 30.1 + - - -
261C ILE* 4.1 0.8 - - - -
262C ILE* 1.3 73.6 - - - +
264C ASN* 1.3 54.3 + - - +
291C LYS* 3.8 5.2 - - - -
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Residues in contact with ASN 264 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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281A TRP* 4.5 9.6 - - + -
284A GLY* 2.8 33.4 + - - -
161C LEU* 4.6 1.0 - - - +
241C MET* 3.5 25.1 - - + +
262C ILE* 4.0 1.0 - - + +
263C SER* 1.3 71.2 + - - +
265C ILE* 1.3 63.5 + - - +
266C ASN* 3.1 31.5 + - - +
268C HIS* 2.8 25.8 + - - -
290C ILE* 5.8 0.7 - - + -
291C LYS 2.7 19.3 + - - +
292C GLY* 3.0 21.2 - - - -
293C GLY 3.2 6.9 + - - -
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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