Contacts of the strand formed by residues 266 - 270 (chain C) in PDB entry 2FVL
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 266 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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8C VAL* 3.7 29.6 - - + -
16C MET* 3.7 19.7 - - - -
17C PRO 3.5 21.8 - - - +
18C VAL* 3.5 19.1 - - + +
48C HIS* 3.9 12.3 - - + -
212C VAL* 4.6 9.9 - - + -
213C LEU 3.2 5.6 + - - +
214C VAL* 3.2 16.7 - - + +
215C ALA 2.7 32.2 + - - -
264C GLY 4.2 2.2 + - - +
265C VAL* 1.3 74.3 - - - +
267C VAL* 1.3 58.0 + - - +
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Residues in contact with VAL 267 (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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18C VAL 3.0 9.6 + - - +
19C LEU* 3.3 19.5 - - + +
20C GLY 2.9 22.4 + - - -
215C ALA* 3.9 4.5 - - + -
218C ALA* 3.3 34.1 - - + -
257C LEU* 3.8 26.7 - - + +
260C GLN* 3.8 23.1 - - + -
261C LEU* 3.8 25.6 - - + -
266C VAL* 1.3 75.4 - - - +
268C LEU* 1.3 64.0 - - - +
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Residues in contact with LEU 268 (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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19C LEU* 5.0 0.2 - - - -
20C GLY* 3.4 25.4 - - - +
22C GLY 4.7 2.2 - - - +
48C HIS* 3.8 23.6 - - + +
50C ASP* 3.6 36.8 - - + +
190C GLN* 3.8 17.9 - - - +
214C VAL* 4.2 8.5 - - + -
215C ALA 3.0 16.2 + - - +
216C HIS* 4.3 4.5 - - + -
218C ALA* 3.6 23.7 + - - +
219C LEU* 5.5 0.2 - - - +
267C VAL* 1.3 75.5 - - - +
269C ALA* 1.3 64.3 + - - +
1002C NAP 3.3 35.4 + - - +
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Residues in contact with ALA 269 (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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19C LEU* 4.7 6.3 - - + -
20C GLY 3.0 11.3 + - - +
21C PHE* 3.7 12.8 - - - -
22C GLY* 3.1 15.2 + - - -
46C PHE* 4.8 2.9 - - + -
219C LEU* 4.5 6.1 - - + -
257C LEU* 4.1 24.2 - - + -
267C VAL 4.3 0.2 + - - -
268C LEU* 1.3 75.8 - - - +
270C LYS* 1.3 61.8 + - - +
280C ASN* 3.9 26.4 + - + +
1002C NAP 3.8 5.6 - - - -
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Residues in contact with LYS 270 (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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22C GLY* 3.4 23.7 - - - +
24C TYR 3.4 25.6 - - - +
25C ALA* 4.9 3.3 - - - +
26C PRO* 5.7 0.6 - - - +
222C GLN* 3.3 20.0 + - - +
269C ALA* 1.3 70.8 - - - +
271C SER* 1.3 61.2 + - - +
272C TYR* 3.6 26.7 - - + +
1002C NAP 2.6 111.3 + - - +
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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